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1

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

PubMed

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

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

2015-02-01

2

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

PubMed

We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-?-carotene (?-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute ?-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of ?-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of ?-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of the observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of ?-carotene with the vibrations of a proximate solvent molecule through solute-solvent dipole-dipole and dipole-quadrupole interactions. It is shown that the infrared active modes arise from the dipole-dipole interaction, whereas Raman active modes from the dipole-quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å. PMID:24880300

Shimada, Rintaro; Hamaguchi, Hiro-o

2014-05-28

3

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

SciTech Connect

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

Shimada, Rintaro; Hamaguchi, Hiro-o, E-mail: hhama@nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan (China)

2014-05-28

4

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

5

Dipole-dipole interaction between rubidium Rydberg atoms  

NASA Astrophysics Data System (ADS)

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 (Förster 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,mj) fine structure levels that have been selectively excited. The data are compared to calculated spectra.

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

2011-11-01

6

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

SciTech Connect

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

Belim, S. M., E-mail: sbelim@mail.ru [Dostoevsky Omsk State University (Russian Federation)

2013-06-15

7

Effective dipole-dipole interactions in critical nanofluids  

NASA Astrophysics Data System (ADS)

It is long known that the effective dipole-dipole coupling is averaged to zero when the spin carrying atoms are involved in a fast random movement in an unconfined fluid. The presented theory shows that if (i) the fluid is confined in long closed nanotubes, (ii) the fluid is in the vicinity of the second order phase transition, and (iii) the mobility of the spin carrying atoms of the fluid is high then the effective dipole-dipole coupling of the fluid is characterized by a finite global value that is independent of the spacing between all the atoms and independent of the length of the nanotubes. We report how the two regimes of the strong and weak effective dipole-dipole couplings in the vicinity and far from the critical point (CP), respectively, can be discriminated in the NMR experiments. Strong enhancements of the signals in the free induction decay, the line shape and the superradiation that result from the abnormally large effective dipole-dipole coupling in the vicinity of the CP are predicted.

Rudavets, M. G.

2013-05-01

8

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

NASA Astrophysics Data System (ADS)

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

El-Ganainy, Ramy; John, Sajeev

2013-08-01

9

Speed of Sound of a Bose-Einstein Condensate with Dipole-Dipole Interactions  

NASA Astrophysics Data System (ADS)

In the present work the case of a chromium Bose-Einstein condensate is considered. The model includes not only the presence of the so-called contact interaction but also a long range and anisotropic dipole-dipole interaction has been included. Some thermodynamical properties are analyzed. For instance, the size of the condensate, chemical potential, speed of sound, number of particles, etc., are deduced. It will be shown that this dipole-dipole interaction implies the emergence of anisotropy, for example, in the speed of sound. The possible use of this anisotropy as a tool for the analysis of dissipative mechanisms, for instance, Landau’s criterion for superfluidity, will be also discussed.

González-Fernández, B.; Camacho, A.

2013-12-01

10

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

E-print Network

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

2011-01-01

11

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

2010-11-01

12

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

13

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

E-print Network

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.

Motohiko Ezawa

2010-07-23

14

Dipole-dipole interaction between a quantum dot and graphene nanodisk  

E-print Network

We study theoretically the dipole-dipole interaction and energy transfer in a hybrid system consisting of a quantum dot and graphene nanodisk embedded in a nonlinear photonic crystal. In our model a probe laser field is applied to measure the energy transfer between the quantum dot and graphene nanodisk while a control field manipulates the energy transfer process. These fields create excitons in the quantum dot and surface plasmon polaritons in the graphene nanodisk which interact via the dipole-dipole interaction. Here the nonlinear photonic crystal acts as a tunable photonic reservoir for the quantum dot, and is used to control the energy transfer. We have found that the spectrum of power absorption in the quantum dot has two peaks due to the creation of two dressed excitons in the presence of the dipole-dipole interaction. The energy transfer rate spectrum of the graphene nanodisk also has two peaks due to the absorption of these two dressed excitons. Additionally, energy transfer between the quantum dot and the graphene nanodisk can be switched on and off by applying a pump laser to the photonic crystal or by adjusting the strength of the dipole-dipole interaction. We show that the intensity and frequencies of the peaks in the energy transfer rate spectra can be modified by changing the number of graphene monolayers in the nanodisk or the separation between the quantum dot and graphene. Our results agree with existing experiments on a qualitative basis. The principle of our system can be employed to fabricate nano-biosensors, optical nano-switches, and energy transfer devices.

Joel D. Cox; Mahi R. Singh; Godfrey Gumbs; Miguel. A. Antón; Fernando Carreño

2012-10-09

15

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

16

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

NASA Astrophysics Data System (ADS)

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

Yu, Yue; Luo, Zhuxi; Wang, Ziqiang

2014-07-01

17

Ising interaction between orbital angular momentum states through magnetic dipole-dipole interaction  

E-print Network

In quantum information processing, one of the most preferred interaction between qubits is Ising type interaction. We propose a scheme to implement exact Ising interaction using orbital angular momentum states of any physical system that has magnetic dipole moment proportional to its angular momentum. If two qubit levels are chosen among highest-M states, magnetic dipole-dipole interaction gives an exact mathematical form of the Ising interaction. Real physical systems applicable to our scheme can possibly be rotational states of molecules, electronic orbital states of atoms, flux states of superconducting rings, or electronic states of nitrogen-vacancy centers in diamond. To investigate the feasibility of our scheme, we present brief analysis on some physical systems.

Sang Jae Yun; Jaewan Kim; Chang Hee Nam

2014-03-11

18

Controlling the dipole-dipole interaction using NMR composite rf pulses  

NASA Astrophysics Data System (ADS)

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

Baudin, Emmanuel

2014-08-01

19

Redistribution of atomic population among nearly degenerate Rydberg states through dipole-dipole interactions  

NASA Astrophysics Data System (ADS)

Ultra-cold highly-excited atoms in a magneto-optical trap are strongly coupled by the dipole-dipole interaction. Rubidium atoms that have been excited to the 32d5/2, |mj| = 1/2 sublevel can exchange energy when an applied static electric field tunes the Stark states into resonance. They do so via the densely packed set of resonant interactions 32d+32d->34p+30g near 0.3 V/cm. Atoms that have exchanged energy and are now in the final p and manifold states can be coupled to a resonance involving 32d5/2, |mj| = 3/2 and 1/2 states, which redistributes population among the |mj| sublevels. We present experimental and computational studies that investigate this redistribution.

Carroll, Thomas J.; Fahey, Donald P.; Noel, Michael W.; Mellus, Alex; Ward, Jon

2012-06-01

20

PHYSICAL REVIEW B 85, 224303 (2012) Mixed-space approach for calculation of vibration-induced dipole-dipole interactions  

E-print Network

; published 19 June 2012) By explicitly taking into account the effects of vibration-induced dipole for the effects of vibration-induced dipole-dipole interactions on the phonon frequencies of an ionic crystalPHYSICAL REVIEW B 85, 224303 (2012) Mixed-space approach for calculation of vibration

Chen, Long-Qing

21

Entangling Dipole-Dipole Interactions for Quantum Logic in Optical Lattices  

NASA Astrophysics Data System (ADS)

The ability to engineer the quantum state of a many-body system represents the ``holy grail" of coherent control and opens the door to a host of new applications and fundamental studies ranging from improvements in precision measurement to quantum computation. At the heart of these quantum-information processing tasks are entangled states. These can be created through a ``quantum-circuit" consisting of a series of simple quantum logic gates acting only on single or pairs of qubits. Any physical implementation of a quantum circuit must contend with an inherent conflict. Qubits must strongly couple to one another and to an external classical field which drives the algorithm, while simultaneously coupling very weakly to the noisy environment which decoheres the quantum superpositions. We have identified a new system for quantum-information processing: ultra-cold trapped neutral atoms (G. K. Brennen et al. ), Phys. Rev. Lett. 82 , 1060 (1999); see also eprint quant- ph/9910031. Neutrals interact very weakly with the environment and coupling between them can be induced on demand through resonant excitation or elastic collisions via direct overlap between wavepackets(D. Jaksch et al.), Phys. Rev. Lett. 82 1975 (1999).. The ability to turn interactions on and off reduces decoherence and the spread of errors amongst qubits. In the implementation presented here I will discuss entangling atoms with electric dipole-dipole interactions in optical lattices (P.S. Jessen and I. H. Deutsch, Adv. At. Mol. Phys. 36), 91 (1996).. These traps provide an extremely flexible environment for coherent control of both internal and external degrees of freedom of atom wave packets as in ion traps(D. Wineland et al.), Fortschr. Phys. 46, 363 (1998).. Dipole-dipole interactions can be coherent when atoms are tightly localized at a distance small compared to the optical wavelength. By inducing dipoles conditional on the logical state of the atoms we can engineer quantum gates. Detailed analysis of the gate fidelity, including some effects of the molecular potentials will be presented.

Deutsch, Ivan

2000-06-01

22

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

23

Observation of suppression of light scattering induced by dipole-dipole interactions in a cold atomic ensemble  

E-print Network

We study the emergence of collective scattering in the presence of dipole-dipole interactions when we illuminate a cold cloud of rubidium atoms with a near-resonant and weak intensity laser. The size of the atomic sample is comparable to the wavelength of light. When we gradually increase the atom number from 1 to 450, we observe a broadening of the line, a small red shift and, consistently with these, a strong suppression of the scattered light with respect to the noninteracting atom case. Numerical simulations, which include the internal atomic level structure, agree with the data.

J. Pellegrino; R. Bourgain; S. Jennewein; Y. R. P. Sortais; S. D. Jenkins; J. Ruostekoski; A. Browaeys

2014-10-08

24

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

E-print Network

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

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

2015-01-12

25

Long-range order in one-dimensional spinless Fermi gas with attractive dipole-dipole interaction  

NASA Astrophysics Data System (ADS)

One-dimensional spinless Fermi gas with attractive dipole-dipole interaction is investigated. Results obtained show that when the interaction is weak, the excitation spectrum is linear and the superconducting correlation function decays as a power law, indicating the validity of the Tomonaga-Luttinger (TL) liquid picture. However, when the interaction reaches a critical value, the excitation spectrum is nonlinear and the superconducting correlation function remains finite for infinity separation, indicating that real long-range order has been established and the breakdown of the TL liquid picture. We prove that the existence of long-range order is not in contradiction with the Hohenberg theorem and show that this system is related to the Kitaev toy model, therefore, it has potential applications for future topological quantum computation.

Yan, Zhongbo; Chen, Liang; Wan, Shaolong

2014-07-01

26

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

NASA Astrophysics Data System (ADS)

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

Saalwächter, Kay

2014-08-01

27

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

E-print Network

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

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

2007-11-02

28

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

PubMed

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

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

2014-08-28

29

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

E-print Network

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

Yavuz, Deniz

30

Geometric quantum discord and entanglement between two atoms in Tavis-Cummings model with dipole-dipole interaction under intrinsic decoherence  

NASA Astrophysics Data System (ADS)

Quantum correlation and entanglement, measured by geometric quantum discord (GQD) and concurrence respectively, between two identical two-level atoms are investigated in detail in Tavis-Cummings model with dipole-dipole interaction (DDI) under intrinsic decoherence. The results show that the phase decoherence rate makes the original harmonic vibration with respective to time decay to a stable value. DDI coupling enhances GQD and corcurrence and even avoids entanglement sudden death (ESD). By the introduction of phase decoherence rate, the atom-light field coupling coefficient makes the decay of periodical curves quicker. Evolution periods are shortened as photon number increases, as well DDI and atomic-light field coupling become stronger. Moreover, both GQD and concurrence have nothing to do with frequency of cavity field and atoms for the resonant case.

Fan, Kai-Ming; Zhang, Guo-Feng

2014-06-01

31

Resonant electric dipole-dipole interactions between cold Rydberg atoms in a magnetic field K. Afrousheh, P. Bohlouli-Zanjani, J. D. Carter, A. Mugford, and J. D. D. Martin  

E-print Network

Resonant electric dipole-dipole interactions between cold Rydberg atoms in a magnetic field K October 2005; published 5 June 2006 Laser-cooled 85 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

Le Roy, Robert J.

32

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  

NASA Astrophysics Data System (ADS)

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 31P-31P distance determinations of numerous crystalline model compounds representing a wide range of dipolar coupling strengths.

Ren, Jinjun; Eckert, Hellmut

2013-04-01

33

Perturbation analyses of intermolecular interactions  

NASA Astrophysics Data System (ADS)

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.

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

2011-08-01

34

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

35

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

PubMed Central

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

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

1990-01-01

36

Dipole-dipole instability of atom clouds in a far-detuned optical dipole trap  

SciTech Connect

The effect of the dipole-dipole interaction on the far-off-resonance optical dipole trapping scheme is calculated by a mean-field approach. The trapping laser field polarizes the atoms and the accompanying dipole-dipole energy shift deepens the attractive potential minimum in a pancake-shaped cloud. At high density the thermal motion cannot stabilize the gas against self-contraction and an instability occurs. We calculate the boundary of the stable and unstable equilibrium regions on a two-dimensional phase diagram of the atom number and the ratio of the trap depth to the temperature. We discuss the limitations imposed by the dipole-dipole instability on the parameters needed to reach Bose-Einstein condensation in an optical dipole trap.

Nagy, D.; Domokos, P. [Research Institute of Solid State Physics and Optics, Hungarian Academy of Sciences, H-1525 Budapest P.O. Box 49 (Hungary)

2007-05-15

37

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

SciTech Connect

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

González, M.; Lemus-Santana, A.A. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Rodríguez-Hernández, J. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Instituto de Ciencia y Tecnología de Materiales, Universidad de La Habana, Havana (Cuba); Aguirre-Velez, C.I. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Knobel, M. [Institute of Physics “Gleb Wataghin”, UNICAMP, 13083-970 Campinas, SP (Brazil); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico)

2013-08-15

38

The diversity of physical forces and mechanisms in intermolecular interactions.  

PubMed

Intermolecular interactions became an inherent part of the structure-function paradigm. Therefore, the generalized concept of protein stability and interactions should consider the balance of stabilizing forces working in different types of intermolecular interactions. We consider here two 'extremes' of protein interactions, viral protein with high intrinsic disorder and hyperthermostable protein complexes. Intermolecular interactions provide folding upon binding as a part of function in the viral case, while they secure and stabilize specific native interfaces as a prerequisite for function in hyperthermostable complexes. We propose a generalized concept of protein stability and interactions, which includes intermolecular interactions comprising distinct combinations of stabilizing forces depending on the types of interacting partners. PMID:21572170

Berezovsky, Igor N

2011-06-01

39

Coherent dipole-dipole coupling between two single atoms at a Förster resonance  

E-print Network

Resonant energy transfers, i.e. the non-radiative redistribution of an electronic excitation between two particles coupled by the dipole-dipole interaction, lie at the heart of a variety of chemical and biological phenomena, most notably photosynthesis. In 1948, F\\"orster established the theoretical basis of fluorescence resonant energy transfer (FRET), paving the ground towards the widespread use of FRET as a "spectroscopic ruler" for the determination of nanometer-scale distances in biomolecules. The underlying mechanism is a coherent dipole-dipole coupling between particles, as already recognized in the early days of quantum mechanics, but this coherence was not directly observed so far. Here, we study, both spectroscopically and in the time domain, the coherent, dipolar-induced exchange of electronic excitations between two single Rydberg atoms separated by a controlled distance as large as 15 microns, and brought into resonance by applying a small electric field. The coherent oscillation of the system between two degenerate pair states occurs at a frequency that scales as the inverse third power of the distance, the hallmark of dipole-dipole interactions. Our results not only demonstrate, at the most fundamental level of two atoms, the basic mechanism underlying FRET, but also open exciting prospects for active tuning of strong, coherent interactions in quantum many-body systems.

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

2014-05-30

40

New approach to mesophase stabilization through hydrogen-bonding molecular interactions in binary mixtures  

SciTech Connect

The authors report a new approach to novel liquid crystalline moieties having a greatly enhanced mesomorphic range through the formation of intermolecular hydrogen bonds between two dissimilar mesogens. In liquid crystals, mesomorphicity results from a proper combination of the shape of a molecule and the magnitude and direction of molecular interactions between molecules. While the importance of dipole-dipole interactions in the formation of mesophases has long been established, we have hypothesized that the occurrence of intermolecular hydrogen bonding should have great potential for ordering thermotropic liquid crystals because H-bonding is much stronger than dipole-dipole interactions.

Kato, T.; Frechet, J.M.J. (Cornell Univ., Ithaca, NY (USA))

1989-10-25

41

The investigation of the hydrogen bond saturation effect during the dipole-dipole induced azobenzene supramolecular self-assembly.  

PubMed

The substituent group and hydrogen bonds play important roles in supramolecular self-assembly. To exploit the influential mechanism of hydrogen bonds during the dipole-dipole induced supramolecular self-assembly, some rigid azobenzene molecules with different electronegativity and hydrogen bonding capabilities were identified and designed. Different regular-shaped architectures were constructed via a simple solution process under mild conditions. Both experimental results and density functional theory calculations show that weak ?-? stacking interactions lead to thick and short nanocylinders, strong dipole-dipole interactions and dipole induced ?-? stacking lead to long and thin nanorods, appropriate hydrogen bonds consolidate the dipole-dipole interactions and dipole induced ?-? stacking, forming thin nanosheets, while excessive hydrogen bonds in azobenzene would ruin the regular-shaped structures, giving irregular and stochastic aggregates. Namely there exists a certain hydrogen bond saturation effect in generating azobenzene nanostructures driven by dipole-dipole interactions. The results indicate that the morphologies of organic materials with azobenzene structures can be effectively controlled through rational molecular design by way of introducing appropriate dipole and hydrogen bonds. PMID:24196867

Li, Linfeng; Wu, Rongliang; Guang, Shanyi; Su, Xinyan; Xu, Hongyao

2013-12-21

42

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.

43

New approach to mesophase stabilization through hydrogen-bonding molecular interactions in binary mixtures  

Microsoft Academic Search

The authors report a new approach to novel liquid crystalline moieties having a greatly enhanced mesomorphic range through the formation of intermolecular hydrogen bonds between two dissimilar mesogens. In liquid crystals, mesomorphicity results from a proper combination of the shape of a molecule and the magnitude and direction of molecular interactions between molecules. While the importance of dipole-dipole interactions in

Takashi Kato; Jean M. J. Frechet

1989-01-01

44

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

45

Intermolecular forces: A solution to dispersion interactions  

NASA Astrophysics Data System (ADS)

London dispersion forces have been cited as an important factor in protein folding, drug-receptor interactions, and catalyst selectivities. However, careful analysis of a model system finds that the dispersion interactions are only minor contributors to the formation of complexes in solution.

Shimizu, Ken D.

2013-12-01

46

Oscillations in dipole-dipole transitions from nearly degenerate Rydberg states  

NASA Astrophysics Data System (ADS)

Pairs of ultracold highly excited atoms can exchange energy over long distances through a dipole-dipole coupling. We present an experimental study of the time dependence of this interaction. Rubidium atoms in a magneto-optical trap are impulsively excited to a coherent superposition of three closely spaced (<10 MHz) 32d5/2 |mj| sublevels. An electric field is used to control the |mj| Stark splitting. Atoms are allowed to exchange energy according to 32d+32d->34p+30f, and the distribution of final states is measured using state selective field ionization. As the time between excitation and ionization is varied, oscillations in the energy exchange are observed. The period of these oscillations is seen to decrease as the initial |mj| state separation is increased.

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

2011-06-01

47

Constraints on exotic dipole-dipole couplings between electrons at the micrometer scale  

E-print Network

New constraints on exotic dipole-dipole interactions between electrons at the micrometer scale are established, based on a recent measurement of the magnetic interaction between two trapped $^{88}$Sr$^+$ ions. For light bosons (mass $\\le$ 0.1 eV) we obtain $90\\%$ confidence intervals on pseudo-scalar and axial-vector mediated interaction strengths of $\\left|g_P^eg_P^e/4\\pi\\hbar c\\right|\\le 1.5\\times 10^{-3}$ and $\\left|g_A^eg_A^e/4\\pi\\hbar c\\right|\\le 1.2\\times 10^{-17}$, respectively. These bounds significantly improve on previous work for this mass range. Assuming CPT invariance, these constraints are compared to those on anomalous electron-positron interactions, derived from positronium hyperfine spectroscopy. For axial-vector mediated interaction the electron-electron constraints are six orders of magnitude more stringent than the electron-positron constraints. Bounds on torsion gravity are also derived and compared with previous work performed at different length scales.

Kotler, Shlomi; Kimball, Derek F Jackson

2015-01-01

48

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

49

Energy decomposition analysis of covalent bonds and intermolecular interactions  

NASA Astrophysics Data System (ADS)

An energy decomposition analysis method is implemented for the analysis of both covalent bonds and intermolecular interactions on the basis of single-determinant Hartree-Fock (HF) (restricted closed shell HF, restricted open shell HF, and unrestricted open shell HF) wavefunctions and their density functional theory analogs. For HF methods, the total interaction energy from a supermolecule calculation is decomposed into electrostatic, exchange, repulsion, and polarization terms. Dispersion energy is obtained from second-order Møller-Plesset perturbation theory and coupled-cluster methods such as CCSD and CCSD(T). Similar to the HF methods, Kohn-Sham density functional interaction energy is decomposed into electrostatic, exchange, repulsion, polarization, and dispersion terms. Tests on various systems show that this algorithm is simple and robust. Insights are provided by the energy decomposition analysis into H2, methane C-H, and ethane C-C covalent bond formation, CH3CH3 internal rotation barrier, water, ammonia, ammonium, and hydrogen fluoride hydrogen bonding, van der Waals interaction, DNA base pair formation, BH3NH3 and BH3CO coordinate bond formation, Cu-ligand interactions, as well as LiF, LiCl, NaF, and NaCl ionic interactions.

Su, Peifeng; Li, Hui

2009-07-01

50

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

51

Intermolecular interactions between doxorubicin and ?-cyclodextrin 4-methoxyphenol conjugates.  

PubMed

Newly synthesized derivatives of ?-cyclodextrin, mono(6-deoxy-6-(1-1,2,3-triazo-4-yl)-1-propane-3-O-(4-methoxyphenyl))?-cyclodextrin (1) and mono(6-deoxy-6thio(1-propane-3-O-(4-methoxyphenyl))) ?-cyclodextrin (2) were designed to be receptors of the anticancer drug doxorubicin, which could potentially decrease the adverse effects of the drug during treatment. In both aqueous and aqueous dimethyl sulfoxide (DMSO) solutions, doxorubicin forms an inclusion complex with the new cyclodextrin derivatives with formation constants of K(s) = 2.3 × 10(4) and K(s) = 3.2 × 10(5) M(-1) for cyclodextrins 1 and 2, respectively. The stabilities of the complexes are 2-3 orders of magnitude greater than those with native ?-cyclodextrin, and the flexibility of the linker of the side group of the cyclodextrins contributes to this stability. In a hydrogen-bond-accepting solvent, such as pure DMSO, an association that includes hydrogen bonding and chloride ions is favored over the binding of doxorubicin in the cavity of the cyclodextrin derivative. This contrasts with an aqueous medium in which a strong inclusion complex is formed. Cyclic voltammetry, UV-vis, (1)H NMR, and molecular modeling studies of solutions in DMSO and of solutions in water/DMSO demonstrated that the two different modes of intermolecular interaction between doxorubicin and the cyclodextrin derivative depended on the solvent system being utilized. PMID:22283628

Swiech, Olga; Mieczkowska, Anna; Chmurski, Kazimierz; Bilewicz, Renata

2012-02-16

52

Controlling intermolecular spin interactions of La@C(82) in empty fullerene matrices.  

PubMed

The ESR properties and crystal structures of solid-state La@C(82) in empty fullerene matrices were investigated by changing the concentration of La@C(82) and the species of an empty fullerene matrix: C(60), C(70), C(78)(C(2v)(3)), C(82)(C(2)) and C(84)(D(2d)(4)). The rotational correlation time of La@C(82) molecules tended to be shorter when La@C(82) is dispersed in larger fullerene matrices because large C(2n) molecules provide more space for La@C(82) molecules for rotating. La@C(82) dispersed in a hcp-C(82) matrix showed the narrowest hyperfine structure (hfs) due to the ordered nature of La@C(82) molecules in the C(82) crystal. On the other hand, in a C(60) matrix, La@C(82) molecules formed clusters because of the large different solubility, which leads to the ESR spectra being broad sloping features due to strong dipole-dipole and exchange interactions. PMID:20126778

Ito, Yasuhiro; Warner, Jamie H; Brown, Richard; Zaka, Mujtaba; Pfeiffer, Rudolf; Aono, Takayuki; Izumi, Noriko; Okimoto, Haruya; Morton, John J L; Ardavan, Arzhang; Shinohara, Hisanori; Kuzmany, Hans; Peterlik, Herwig; Briggs, G Andrew D

2010-02-21

53

Competing intermolecular interactions in some 'bridge-flipped' isomeric phenylhydrazones.  

PubMed

To examine the roles of competing intermolecular interactions in differentiating the molecular packing arrangements of some isomeric phenylhydrazones from each other, the crystal structures of five nitrile-halogen substituted phenylhydrazones and two nitro-halogen substituted phenylhydrazones have been determined and are described here: (E)-4-cyanobenzaldehyde 4-chlorophenylhydrazone, C(14)H(10)ClN(3), (Ia); (E)-4-cyanobenzaldehyde 4-bromophenylhydrazone, C(14)H(10)BrN(3), (Ib); (E)-4-cyanobenzaldehyde 4-iodophenylhydrazone, C(14)H(10)IN(3), (Ic); (E)-4-bromobenzaldehyde 4-cyanophenylhydrazone, C(14)H(10)BrN(3), (IIb); (E)-4-iodobenzaldehyde 4-cyanophenylhydrazone, C(14)H(10)IN(3), (IIc); (E)-4-chlorobenzaldehyde 4-nitrophenylhydrazone, C(13)H(10)ClN(3)O(2), (III); and (E)-4-nitrobenzaldehyde 4-chlorophenylhydrazone, C(13)H(10)ClN(3)O(2), (IV). Both (Ia) and (Ib) are disordered (less than 7% of the molecules have the minor orientation in each structure). Pairs (Ia)/(Ib) and (IIb)/(IIc), related by a halogen exchange, are isomorphous, but none of the 'bridge-flipped' isomeric pairs, viz. (Ib)/(IIb), (Ic)/(IIc) or (III)/(IV), is isomorphous. In the nitrile-halogen structures (Ia)-(Ic) and (IIb)-(IIc), only the bridge N-H group and not the bridge C-H group acts as a hydrogen-bond donor to the nitrile group, but in the nitro-halogen structures (III) (with Z' = 2) and (IV), both the bridge N-H group and the bridge C-H group interact with the nitro group as hydrogen-bond donors, albeit via different motifs. The occurrence here of the bridge C-H contact with a hydrogen-bond acceptor suggests the possibility that other pairs of `bridge-flipped' isomeric phenylhydrazones may prove to be isomorphous, regardless of the change from isomer to isomer in the position of the N-H group within the bridge. PMID:22763695

Ojala, William H; Arola, Trina M; Brigino, Ann M; Leavell, Jeremy D; Ojala, Charles R

2012-07-01

54

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

55

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

NASA Astrophysics Data System (ADS)

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

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

2014-07-01

56

Influence of intermolecular interactions on spectroscopic characteristics of metal nanoparticles and their composites.  

PubMed

In this paper we investigate the possibility to apply the concepts of non-specific intermolecular interactions and dispersive local field effect approach for study of the influence of interactions of metal nanoparticles with matrix molecules on the spectral characteristics of composites. The effect of intermolecular (interparticle) interactions and the influence of the dielectric environment on the peak position of the plasmon resonance band of colloidal solutions and thin films formed from noble metal nanostructures is determined. Simulated and experimental absorption spectra obtained for a colloidal solution of silver and gold nanoparticles, of various shapes and sizes in water and glycerol, are in good agreement. PMID:25310112

Shaganov, Igor I; Perova, Tatiana S; Mukhina, Maria V; Martynenko, Irina V; Baranov, Alexander V; Fedorov, Anatoly V; Gerard, Valerie; Gun'ko, Yuri K

2014-11-28

57

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. PMID:24121340

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

2013-01-01

58

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. PMID:18572937

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

2010-01-01

59

Adsorption in zeolites: intermolecular interactions and computer simulation  

Microsoft Academic Search

The input to a simulation is the potential energy model. In microporous solids, the adsorbate adsorbent interaction is the most significant part of the total potential energy. The full scale semi-empirical PN model is summarised as an example of a state of the art potential model. The potential includes damped two-body dispersion interactions, three-body interactions, induced interactions (often negligibly small)

David Nicholson; Roland J.-M. Pellenq

1998-01-01

60

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

61

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

E-print Network

Experimental Charge Densities and Intermolecular Interactions: Electrostatic and Topological Analysis of DL-Histidine Philip Coppens,*, Yuriy Abramov, Michael Carducci,,1 Boris Korjov, Irina-resolution, low-temperature X-ray diffraction data set on DL-histidine, collected with a CCD detector, is used

Coppens, Philip

62

Probing weak intermolecular interactions by using the invariom approach: a comparative study of s-tetrazine.  

PubMed

A comparative study of chemical bonding peculiarities in 1,2,4,5-tetrazine was carried out to test the performance of a recently developed invariom approach against a conventional charge density analysis of high-resolution X-ray diffraction data and quantum chemical calculations within the plane-wave functional theory. The amazing similarity between the intermolecular features thus obtained for this van der Waals crystal showed the invariom approximation to now emerge as a fast and convenient way towards reliable description of weak intermolecular interactions. PMID:24737643

Nelyubina, Yulia V; Korlyukov, Alexander A; Lyssenko, Konstantin A

2014-06-01

63

Experimental and computational investigation of intermolecular interactions in cyclopentanone with methanol mixture  

NASA Astrophysics Data System (ADS)

In this Letter, excess molar volumes, refractive index deviations, Raman spectra and quantum-chemical calculations have been used to explore the underlying intermolecular interactions in the binary mixture containing cyclopentanone (CPN) and methanol. The experimental data reveal that the 1:1 (Ia) and 1:2 (Ib) cross-associations between CPN and methanol are formed in the studied binary mixture. This result has been further corroborated via theoretical calculations. In addition, the observed 1747 and 1732 cm-1 bands can be assigned to the Cdbnd O stretching vibrations of the intermolecular cross-associations Ia and Ib, respectively, in distinct contradiction with the previous explanations.

Zhang, Yu-Feng; Huang, Rong-Yi; Wang, Jun-Wei; Geng, Tong-Mou; Zhao, Shun-Ping; Wu, Gen-Hua

2014-09-01

64

Intermolecular Interactions, Nucleation, and Thermodynamics of Crystallization of Hemoglobin C  

Microsoft Academic Search

The mutated hemoglobin HbC (?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

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

2002-01-01

65

Effects of three-body intermolecular interactions on the nematic—paranematic phase diagram  

Microsoft Academic Search

An extension of the Maier—Saupe theory of the nematic—isotropic transition in liquid crystals, which incorporates three-body intermolecular interactions into the effective single-particle pseudopotential, is presented. Numerical calculations based on this theory are performed to investigate the effect of these three-body interactions on the nematic—isotropic transition in zero field, on the nematic—paranematic coexistence curve in the presence of an applied field,

John R. De Bruyn

1992-01-01

66

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

SciTech Connect

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

Han, Heekyung [Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 3M7 (Canada); Wardlaw, David M., E-mail: dwardlaw@mun.ca [Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1C 5S7 (Canada); Frolov, Alexei M., E-mail: afrolov@uwo.ca [Department of Applied Mathematics, University of Western Ontario, London, Ontario N6H 5B7 (Canada)

2014-05-28

67

Assessing intermolecular RNA:RNA interactions within a ribonucleoprotein complex using heavy metal cleavage mapping.  

PubMed

Heavy metal cleavage mapping analysis of both assembling and fully mature ribonucleoprotein (RNP) complexes are informative techniques for assessing the intermolecular base pairing between small non-coding RNAs and their interacting target RNAs. Lead cleavage of the RNA in partially or fully assembled RNPs in the absence or presence of the interacting RNA can determine both the accessibility of the base pairing sequence within the RNP itself as well as its interaction with the target RNA. In this chapter, we detail how this technique was used to map the intermolecular RNA:RNA base pairing of a box C/D RNA with its target RNA within the assembling archaeal RNP complex. PMID:25352141

Gagnon, Keith T; Maxwell, E Stuart

2015-01-01

68

Intermolecular interactions in the bilirubin-cholate-silica system  

NASA Astrophysics Data System (ADS)

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

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

2007-06-01

69

Accurate First Principles Model Potentials for Intermolecular Interactions  

NASA Astrophysics Data System (ADS)

The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

Gordon, Mark S.; Smith, Quentin A.; Xu, Peng; Slipchenko, Lyudmila V.

2013-04-01

70

Accurate first principles model potentials for intermolecular interactions.  

PubMed

The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed. PMID:23561011

Gordon, Mark S; Smith, Quentin A; Xu, Peng; Slipchenko, Lyudmila V

2013-01-01

71

Intermolecular interactions between a Ru complex and organic dyes in cosensitized solar cells: a computational study.  

PubMed

Intermolecular interactions in cyclometalated Ru complex dye (FT89) dimers, carbazole organic dye (MK-45 and MK-111) dimers, FT89-MK-45 complexes, and FT89-MK-111 complexes were investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT) to elucidate the improvement mechanism of dye-sensitized solar cell (DSSC) performance due to cosensitization with FT89 and MK dyes. All of the dimers and complexes form intermolecular cyclic hydrogen bonds via the carboxyl groups. The FT89 dimer and complexes with the TiO2Na model system promote intermolecular interactions with I2via the NCS ligand of the FT89 monomer. The computational results verify that MK-111 behaves not only as a sensitizer but also inhibits FT89 aggregation by effectively serving as a coadsorbent similar to deoxycholic acid (DCA) in the dye solution, suppressing recombination of the injected electrons in TiO2 with I2, improving DSSC performance. PMID:24968132

Kusama, Hitoshi; Funaki, Takashi; Koumura, Nagatoshi; Sayama, Kazuhiro

2014-08-14

72

Intermolecular interactions in binary system of 1-methylimidazole with methanol: A volumetric and theoretical investigation  

NASA Astrophysics Data System (ADS)

The Letter demonstrates an experimental and computational investigation of intermolecular interactions in binary system of 1-methylimidazole (MeIm) with methanol. The densities of binary system were measured at T = 288.15-323.15 K, and the values of excess molar volumes were obtained as a function of composition at each temperature. The experimental results indicate the formation of strong cross-associated complex in the binary system. Meanwhile, the nature of hydrogen bond of the associated complexes was explored based on theoretical calculations. In addition, the changes of thermodynamic properties from the monomers to cross-associated complex were also investigated.

Guo, Chang; Fang, Hui; Huang, Rong-Yi; Xu, Heng; Wu, Gen-Hua; Ye, Shi-Yong

2013-11-01

73

Intermolecular TlH-C anagostic interactions in luminescent pyridyl functionalized thallium(i) dithiocarbamates.  

PubMed

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

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

2014-12-23

74

Effect of Nonadditive Repulsive Intermolecular Interactions on the Light Scattering of Concentrated Protein–Osmolyte Mixtures  

PubMed Central

The static light scattering of three globular proteins, bovine serum albumin, ovalbumin, and ovomucoid, and binary mixtures of each protein and trimethylamine oxide (TMAO) containing between 10 and 70% protein, were measured as a function of total weight per volume concentration up to 100 g/L. The observed dependence of scattering upon concentration may be accounted for quantitatively by an effective hard sphere model incorporating an extension that takes into account the nonadditive nature of the repulsive intermolecular interaction between protein and TMAO. PMID:21175126

Fernández, Cristina; Minton, Allen P.

2012-01-01

75

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

PubMed Central

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

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

2014-01-01

76

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

PubMed

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

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

2013-12-31

77

Practical aspects of wavelength ratiometry in the studies of intermolecular interactions  

NASA Astrophysics Data System (ADS)

Wavelength ratiometry (often abbreviated as ?-ratiometry) is one of the most popular methods to study intermolecular interactions that allows obtaining both thermodynamic and kinetic parameters and can be applied in a variety of sensing and imaging technologies. In comparison with simple recording of intensity it allows avoiding many technical problems and realizing many new possibilities. Here we briefly analyze different approaches in ?-ratiometric sensing that use single, double and multiple fluorescence emitters that are based on different mechanisms producing spectroscopic change and concentrate on their practical aspects. Finally we present several examples of successful application of this method and discuss the prospects for its further development.

Demchenko, Alexander P.

2014-12-01

78

Study on the effects of intermolecular interactions on firefly multicolor bioluminescence.  

PubMed

Firefly luciferase exhibits a color-tuning mechanism based on pH-induced changes in the structure of the active site. These changes increase the polarity of the active site, and thus modulate the intermolecular interactions between the light emitter and active site molecules. In this study, the effects exerted by adenosine monophosphate (AMP), water molecules, and amino acids of Luciola cruciata luciferase active site on the emission wavelength of oxyluciferin were assessed by TD-DFT calculations. The redshift results mainly from decreased interaction of oxyluciferin with AMP and increased interaction of the emitter with a water molecule and Phe249. Breaking of a hydrogen bond between the benzothiazole oxygen atom with formation of a similar bond to the thiazolone oxygen atom is also instrumental. PMID:21919180

da Silva, Luís Pinto; da Silva, Joaquim C G Esteves

2011-11-18

79

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. PMID:22365602

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

2012-01-01

80

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

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

81

Effect of Intermolecular Interactions on the Carbon 1s Near Edge X-ray Absorption Fine Structure (NEXAFS) Spectroscopy of n-Alkanes.  

E-print Network

??“Matrix effects” in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy are the spectroscopic changes induced by intermolecular interactions, providing sensitivity to local structure and… (more)

Neelakanni mudiyanselage, Sahan

2014-01-01

82

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

E-print Network

Atoms K. Afrousheh, P. Bohlouli-Zanjani, D. Vagale, A. Mugford, M. Fedorov, and J. D. D. Martin between cold Rydberg atoms were observed using microwave spectroscopy. Laser-cooled 85Rb atoms pulse transferred a fraction of these Rydberg atoms to the 46p3=2 state. A second microwave pulse

Le Roy, Robert J.

83

Unrestricted absolutely localized molecular orbitals for energy decomposition analysis: Theory and applications to intermolecular interactions involving radicals  

NASA Astrophysics Data System (ADS)

Radical-closed shell and radical-radical intermolecular interactions are less well-understood than those between closed shell species. With the objective of gaining additional insight, this work reports a generalization of the absolutely localized molecular orbital (ALMO) energy decomposition analysis (EDA) to open shell fragments, described by self-consistent field methods, such as standard density functional theory. The ALMO-EDA variationally partitions an intermolecular interaction energy into three separate contributions; frozen orbital interactions, polarization, and charge transfer. The first examples involve comparison of the interactions of alkanes and alkyl radicals (methyl radical, methane, tertiary butyl radical, and isobutane) with sodium, potassium, hydronium, and ammonium cations. A second series of examples involve benzene cation interacting with a series of nucleophiles in both on-top and side-on geometries. The ALMO-EDA yields a variety of interesting insights into the relative roles of its component contributions as the interacting partners and their geometries are changed.

Horn, Paul R.; Sundstrom, Eric Jon; Baker, Thomas A.; Head-Gordon, Martin

2013-04-01

84

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; de Azevedo, Eduardo Ribeiro; Sommer, Michael; Wicklein, André; Thelakkat, Mukundan; Hempel, Günter; Saalwächter, Kay

2013-09-16

85

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials.  

PubMed

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. PMID:19090563

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

86

Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations  

SciTech Connect

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

Kroeger, Ingo; Stadtmueller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian [Peter Gruenberg Institut (PGI-3), Forschungszentrum Juelich, 52425 Juelich (Germany); Juelich-Aachen Research Alliance (JARA) - Fundamentals of Future Information Technology, 52425 Juelich (Germany)

2011-12-21

87

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

PubMed

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

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

2014-01-01

88

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

PubMed

The intermolecular interaction of prednisolone with bovine serum albumin (BSA) was studied using fluorescence, circular dichroism (CD) and molecular docking methods. The experimental results showed that the fluorescence quenching of the BSA at 338 nm by prednisolone resulted from the formation of prednisolone-BSA complex. The number of binding sites (n) for prednisolone binding on BSA was approximately equal to 1. Base on the sign and magnitude of the enthalpy and entropy changes (?H(0)=-149.6 kJ mol(-1) and ?S(0)=-370.7 J mol(-1)K(-1)) and the results of molecular docking, it could be suggested that the interaction forces were mainly Van der Waals and hydrogen bonding interactions. Moreover, in the binding process of BSA with prednisolone, prednisolone molecule can be inserted into the hydrophobic cavity of subdomain IIIA (site II) of BSA. The distance between prednisolone and Trp residue of BSA was calculated as 2.264 nm according to Forster's non-radiative energy transfer theory. PMID:23261625

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

2013-02-15

89

Electric quadrupole moment of graphene and its effect on intermolecular interactions.  

PubMed

Carbon atoms in aromatic compounds exhibit a permanent electric quadrupole moment due to the aromatic ? electron distribution. In the case of small aromatic hydrocarbons, this quadrupole contributes significantly to their intermolecular interactions, but when the honeycomb lattice is expanded to infinity, the quadrupolar field sums to zero and its significance vanishes. Therefore, electrostatic interactions with graphene are often omitted in force field molecular modeling. However, for a finite sheet, the electrostatic field decays only slowly with increasing size and is always non-negligible near edges. In addition, in a corrugated graphene sheet, the electrostatic field near the surface does not vanish completely and remains sizeable. In the present study, we investigated the magnitude of the graphene quadrupolar field as a function of model size and graphene corrugation, and estimated the error resulting from its neglect in molecular dynamics simulations. Exfoliation energies in benzene and hexafluorobenzene were calculated using the potential of mean force method with and without explicit quadrupoles. The effect on exfoliation energies was found to be quite small. However, the quadrupole moment may be important for graphene sheet association (aggregation) as it affects barrier heights, and consequently kinetics of association. Our results indicate that quadrupolar interactions may need to be considered in molecular modeling when graphene is corrugated or bent. PMID:24407154

Kocman, Mikuláš; Pykal, Martin; Jure?ka, Petr

2014-02-21

90

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

91

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

92

Dimensionality of intermolecular interactions in layered crystals by electronic-structure theory and geometric analysis.  

PubMed

Two-dimensional (2D) and layered structures gained a lot of attention in the recent years ("post-graphene era"). The chalcogen cyanides S(CN)2 and Se(CN)2 offer themselves as interesting model systems to study layered inorganic crystal structures; both are built up from cyanide molecules connected by chalcogen bonds (ChBs). Here, we investigate ChBs and their cooperativity directly within the layers of the S(CN)2 and Se(CN)2 crystal structures and, furthermore, in putative O(CN)2 and Te(CN)2 crystal structures derived therefrom. Moreover, we determine the energetic contributions of ChBs within the layers to the overall stabilization energy. To compare these structures not only energetically but also geometrically, we derive a direction-dependent root mean square of the Cartesian displacement, a possible tool for further computational investigations of layered compounds. The molecular chains connected by ChBs are highly cooperative but do not influence each other when combined to layers: the ChBs are nearly orthogonal in terms of energy when connected to the same chalcogen acceptor atom. Layers built up from ChBs account for 41% to 79% of the overall interaction energy in the crystal. This provides new, fundamental insight into the meaning of ChBs, and therefore directed intermolecular interactions, for the stability of crystal structures. PMID:25363246

George, Janine; Deringer, Volker L; Dronskowski, Richard

2015-02-01

93

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

PubMed

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2?/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. PMID:24361848

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

2014-03-01

94

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

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

95

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

SciTech Connect

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

Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw [Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan (China)

2013-11-21

96

Resonance dynamical intermolecular interaction in the crystals of pure and binary mixture n-paraffins  

NASA Astrophysics Data System (ADS)

In the present paper, we report temperature dependent FTIR spectra studies of Davydov splitting value for CH 2 rocking vibrations of pure crystalline n-paraffins C nH 2 n+2 ( n is the number of carbon atoms) and some isomorphically substituted binary mixtures of n-paraffins C 22H 46:C 24H 50. Temperature dependencies of Davydov splitting value have been shown to be characterized by the amount of irregularities (sharp decreasing), which corresponds to the phase transitions into the high-temperature (hexagonal) state for pure n-paraffins or different rotator crystalline states for the mixtures. Statistic and dynamic models have been proposed, which provides an adequate description of the observed effect. In the framework of these models, two different mechanisms are responsible for the temperature behavior of the vibrational mode splitting value. Besides the thermal expansion of crystals at heating, the quenching of vibrational excitons on the orientational defects of different nature takes place, accompanied with the breakage of the crystal lattice translational symmetry. The creation of such defects is resulted from the excitation of librational and rotational molecular degrees of freedom at the crystal polymorphic transitions into different rotary crystalline states. The manifestation of the resonance dynamical intermolecular interaction in the spectra of intramolecular vibrations in these crystals has been theoretically analyzed in terms of stochastic equations, taking into consideration the above mentioned phase transition. We have obtained the explicit expression for the theoretically predicted dependence of Davydov splitting value on temperature. The absorption bands, corresponding to Davydov splitting components, have been shown to approach rapidly each other at the transition to the high-temperature (hexagonal) phase. Computer simulation of such dependence has been performed for some aliphatic compounds. Good agreement between the experimental and computer simulation results has been obtained. The theoretical approach developed in the present paper for the resonance dynamical intermolecular interaction near such transitions from the three-dimensional to one-dimensional phase of crystalline n-paraffins has a general character and can be applied to the description of some specific features observed in the vibrational spectra of rotary crystals.

Puchkovska, G. O.; Danchuk, V. D.; Makarenko, S. P.; Kravchuk, A. P.; Kotelnikova, E. N.; Filatov, S. K.

2004-12-01

97

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

PubMed Central

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

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

1994-01-01

98

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

PubMed Central

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

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

2011-01-01

99

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

NASA Astrophysics Data System (ADS)

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

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

2011-03-01

100

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

NASA Astrophysics Data System (ADS)

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

Sweeney, J. J.; Felske, D.

2013-12-01

101

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

102

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

PubMed

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

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

2010-03-01

103

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

PubMed Central

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

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

2006-01-01

104

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

PubMed

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single ?-pair (C2H4) and two ?-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the ?-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the ?-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved. PMID:25296807

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

2014-10-01

105

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

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

106

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

NASA Astrophysics Data System (ADS)

The scaled versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys. 141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions - Mie, Lennard-Jones, Morse, and Buckingham exponential-6 - have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X-(H2O), X = F, Cl, Br, I, and alkali metal-water, M+(H2O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits to the ab initio data that are between one and two orders of magnitude better in the ?2 than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. The fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.

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

2014-08-01

107

Intermolecular electronic interactions in the primary charge separation in bacterial photosynthesis  

Microsoft Academic Search

In this paper the intermolecular overlap approximation is used to calculate the relative magnitudes of the electronic transfer integrals between the excited singlet state (¹P*) of the bacteriochlorophyll dimer (P) and the accessory bacteriochlorophyll (B) and between B⁻ and bacteriopheopytin (H), along the L and M subunits of the reaction center (RC) of Rps. viridis. The ratio of the electron-transfer

M. Plato; K. Moebius; M. E. Michel-Beyerle; M. Bixon; Joshua. Jortner

1988-01-01

108

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...

109

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

SciTech Connect

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

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

2014-08-14

110

Cooperativity of anion⋯? and ?⋯? interactions regulates the self-assembly of a series of carbene proligands: Towards quantitative analysis of intermolecular interactions with Hirshfeld surface  

NASA Astrophysics Data System (ADS)

The cooperative effect of weak non-covalent forces between anions and electron deficient aromatics by ?⋯? stacking of a series of carbene proligands (1-3) have been thoroughly explored by crystallographic studies. Structural analysis revealed that the anion⋯? and ?⋯? interactions along with intermolecular hydrogen bonding mutually cooperate to facilitate the assembling of the supramolecular framework. The ?⋯? and corresponding anion⋯? interactions have been investigated in the title carbene proligands despite their association with counter ions. The presence of the anion in the vicinity of the ?-system leads to the formation of anion⋯?/?⋯?/?⋯anion network for an inductive stabilization of the assemblies. To assess the dimensionality of the supramolecular framework consolidated by cooperative anion⋯?/?⋯? interactions and hydrogen bonding, different substituent effects in the carbene backbone have been considered to tune these interactions. These facts show that the supramolecular framework based on these cooperative weak forces may be robust enough for application in molecular recognition. The investigation of close intermolecular interactions between the molecules via Hirshfeld surface analyses is presented in order to reveal subtle differences and similarities in the crystal structures. The decomposition of the fingerprint plot area provides a percentage of each intermolecular interaction, allowing for a quantified analysis of close contacts within each crystal.

Samanta, Tapastaru; Dey, Lingaraj; Dinda, Joydev; Chattopadhyay, Shyamal Kumar; Seth, Saikat Kumar

2014-06-01

111

APPLICATIONS OF LASERS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Picosecond spectroscopy of specific intermolecular interactions in dye solutions  

NASA Astrophysics Data System (ADS)

Picosecond spectroscopy was used to investigate an intermolecular hydrogen bond between an impurity center and a solvent. The proposed method for determination of the spectral dependence of the rotational relaxation time of molecules was used to find the inhomogeneous broadening of the spectra of dye solutions governed by the impurity-solvent interaction. The influence of the microstructure of the environment on the rotation of molecules in binary solvents was observed. An investigation was made of the influence of temperature on the rate of formation and dissociation of complexes in an excited state.

Rubinov, Anatolii N.; Bushuk, Boris A.; Stupak, A. P.

1987-12-01

112

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

PubMed

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

Rezler, Mateusz; ?o?ek, Teresa; Wolska, Irena; Maciejewska, Dorota

2014-10-01

113

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

PubMed Central

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

Rezler, Mateusz; ?o?ek, Teresa; Wolska, Irena; Maciejewska, Dorota

2014-01-01

114

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

PubMed

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

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

2012-01-01

115

A method based on the DAOSD approach to estimate the variation of the peak position and bandwidth caused by intermolecular interactions  

NASA Astrophysics Data System (ADS)

Subtle spectral variations caused by intermolecular interactions, which are hardly observed in the original one-dimensional spectra or the second derivative spectra, can be distinctly visualized via spectral patterns in two-dimensional spectra generated by using double asynchronous orthogonal sample designed scheme (DAOSD). If intermolecular interaction only brings about band-shift on a characteristic peak, a pair of cross peaks appears in the corresponding near diagonal region. If intermolecular interaction induces variation of bandwidth only, a cluster of cross peaks forms a diamond pattern in the near diagonal region. In both cases, the variation of peak position or bandwidth can be deduced quantitatively from the pattern of cross peaks. If intermolecular interaction causes variations on both peak position and bandwidth, four cross peaks form a butterfly pattern. In this case, however, it is not straightforward to estimate the variation of peak position and bandwidth directly from the patterns of the cross peaks. In this paper, we propose an algorithm to estimate the variations of peak position and bandwidth of a characteristic peak caused by intermolecular interactions. The validity of this approach was confirmed by computer simulation on several model systems.

Bi, Quan; Chen, Jing; Li, Xiaopei; Shi, Jia-Jia; Guo, Ran; Zhai, Yanjun; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

2014-07-01

116

A theoretical base for optimising intermolecular interactions driving polarity formation in channel-type host guest materials  

NASA Astrophysics Data System (ADS)

Spontaneous polarity formation in channel-type host-guest materials is analysed by a Markov model of growth. Criteria for the strength of collinear intermolecular interaction energies Eij between acceptor-?-donor (A-?-D) guest molecules are discussed in order to optimise characteristic properties of the system. In the case of bulk growth, the sequence EAA? EAD? EDD is producing (i) high values of net polarity nnet, (ii) a low number of attachments q to reach constant values of nnet, and (iii) a low density of orientational defects ? within polar chains. Similarly, the optimum sequence for the growth of oriented films on substrates featuring uniform interactions to guest molecules is: EAA> EDD? EAD.

Quintel, Andrea; Hulliger, Jürg

1999-10-01

117

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

NASA Astrophysics Data System (ADS)

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

Elangovan, S.; Mullainathan, S.

2014-04-01

118

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

PubMed

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

Ingrosso, Francesca; Ladanyi, Branka M

2013-01-17

119

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

120

Effect of Intra-molecular Disorder and Inter-molecular Electronic Interactions on the Electronic Structure of Poly-p-Phenylene Vinylene (PPV)  

E-print Network

We investigate the role of intra-molecular conformational disorder and inter-molecular electronic interactions on the electronic structure of disorder clusters of poly-p-phenylene vinylene (PPV) oligomers. Classical molecular dynamics is used to determine probable molecular geometries, and first-principle density functional theory (DFT) calculations are used to determine electronic structure. Intra-molecular and inter-molecular effects are disentangled by contrasting results for densely packed oligomer clusters with those for ensembles of isolated oligomers with the same intra-molecular geometries. We find that electron trap states are induced primarily by intra-molecular configuration disorder, while the hole trap states are generated primarily from inter-molecular electronic interactions.

Ping Yang; Enrique R. Batista; Sergei Tretiak; Avadh Saxena; Richard L. Martin; D. L. Smith

2007-07-13

121

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

PubMed

High viscosity of monoclonal antibody formulations at concentrations ?100 mg/mL can impede their development as products suitable for subcutaneous delivery. The effects of hydrophobic and electrostatic intermolecular interactions on the solution behavior of MAB 1, which becomes unacceptably viscous at high concentrations, was studied by testing 5 single point mutants. The mutations were designed to reduce viscosity by disrupting either an aggregation prone region (APR), which also participates in 2 hydrophobic surface patches, or a negatively charged surface patch in the variable region. The disruption of an APR that lies at the interface of light and heavy chain variable domains, VH and VL, via L45K mutation destabilized MAB 1 and abolished antigen binding. However, mutation at the preceding residue (V44K), which also lies in the same APR, increased apparent solubility and reduced viscosity of MAB 1 without sacrificing antigen binding or thermal stability. Neutralizing the negatively charged surface patch (E59Y) also increased apparent solubility and reduced viscosity of MAB 1, but charge reversal at the same position (E59K/R) caused destabilization, decreased solubility and led to difficulties in sample manipulation that precluded their viscosity measurements at high concentrations. Both V44K and E59Y mutations showed similar increase in apparent solubility. However, the viscosity profile of E59Y was considerably better than that of the V44K, providing evidence that inter-molecular interactions in MAB 1 are electrostatically driven. In conclusion, neutralizing negatively charged surface patches may be more beneficial toward reducing viscosity of highly concentrated antibody solutions than charge reversal or aggregation prone motif disruption. PMID:25559441

Nichols, Pilarin; Li, Li; Kumar, Sandeep; Buck, Patrick M; Singh, Satish K; Goswami, Sumit; Balthazor, Bryan; Conley, Tami R; Sek, David; Allen, Martin J

2015-01-01

122

Intermolecular interactions in complex liquids: effective fragment potential investigation of water-tert-butanol mixtures.  

PubMed

Structure and bonding patterns in tert-butanol (TBA)-water mixtures are investigated by using molecular dynamics simulations with the effective fragment potential (EFP) method. EFP is a model potential in which all parameters are obtained from a set of ab initio calculations on isolated fragment molecules. Mixed-basis EFP potentials (called "EFPm") for water and TBA molecules were prepared and tested in this work. The accuracy of these EFP potentials is justified by comparison of structures and binding energies in water, TBA, and water-TBA dimers with MP2/6-311++G(d,p) data. It has been found that the discrepancies between EFP and MP2 do not exceed 0.1 Å in intermolecular distances and 1 kcal/mol in binding energies. Structures of TBA-water solutions with 0.0, 0.06, 0.11, 0.16, and 0.50 TBA mole fractions were analyzed by using radial distribution functions (RDFs) and coordination numbers. These results suggest that, at low TBA concentrations, the structure of water is enhanced and water and TBA are not homogeneously mixed at the molecular level. In the equimolar TBA-water solution, the microscopic mixing is more complete. Analysis of the energy components in TBA-water solutions shows that, while the electrostatic and exchange-repulsion terms provide the largest contributions to the total potential energy, the relative importance of the polarization and dispersion terms depends on the concentration of TBA. With an increase of TBA concentration, the fraction of the dispersion energy increases, while the fraction of polarization energy diminishes. However, both polarization and dispersion terms are essential for accurate description of these systems. PMID:22324786

Hands, Michael D; Slipchenko, Lyudmila V

2012-03-01

123

Intermolecular interaction in the OH He and OH Ne open-shell ionic complexes: Infrared predissociation spectra of the 1 and 1 b vibrations  

E-print Network

characterized by microwave,19,20 far-infrared,21­23 midinfrared,18,24 and UV spectroscopy,25 and by ab initioIntermolecular interaction in the OH ­He and OH ­Ne open-shell ionic complexes: Infrared complexes have been recorded by photofragmentation spectroscopy in a tandem mass spectrometer. The 1

Nizkorodov, Sergey

124

Intermolecular electronic interactions in the primary charge separation in bacterial photosynthesis  

SciTech Connect

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

Plato, M.; Moebius, K.; Michel-Beyerle, M.E.; Bixon, M.; Jortner, J. (Freie Universitaet Berlin (West Germany))

1988-10-26

125

Regulatory R region of the CFTR chloride channel is a dynamic integrator of phospho-dependent intra- and intermolecular interactions  

PubMed Central

Intrinsically disordered proteins play crucial roles in regulatory processes and often function as protein interaction hubs. Here, we present a detailed characterization of a full-length disordered hub protein region involved in multiple dynamic complexes. We performed NMR, CD, and fluorescence binding studies on the nonphosphorylated and highly PKA-phosphorylated human cystic fibrosis transmembrane conductance regulator (CFTR) regulatory region, a ?200-residue disordered segment involved in phosphorylation-dependent regulation of channel trafficking and gating. Our data provide evidence for dynamic, phosphorylation-dependent, multisite interactions of various segments of the regulatory region for its intra- and intermolecular partners, including the CFTR nucleotide binding domains 1 and 2, a 42-residue peptide from the C terminus of CFTR, the SLC26A3 sulphate transporter and antisigma factor antagonist (STAS) domain, and 14-3-3?. Because of its large number of binding partners, multivalent binding of individually weak sites facilitates rapid exchange between free and bound states to allow the regulatory region to engage with different partners and generate a graded or rheostat-like response to phosphorylation. Our results enrich the understanding of how disordered binding segments interact with multiple targets. We present structural models consistent with our data that illustrate this dynamic aspect of phospho-regulation of CFTR by the disordered regulatory region. PMID:24191035

Bozoky, Zoltan; Krzeminski, Mickael; Muhandiram, Ranjith; Birtley, James R.; Al-Zahrani, Ateeq; Thomas, Philip J.; Frizzell, Raymond A.; Ford, Robert C.; Forman-Kay, Julie D.

2013-01-01

126

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

127

Intermolecular interaction in density functional theory: Application to carbon nanotubes and fullerenes  

NASA Astrophysics Data System (ADS)

A theoretical study of weak interactions in graphitic materials such as carbon nanotubes (CNTs), fullerenes, and graphene is presented here. Based on a localized orbital density-functional theory formalism, our treatment which has already been applied for graphene-graphene interaction describes independently the weak chemical as well as the van der Waals interactions with high accuracy. The weak chemical interaction is described in the frame of the linear combination of atomic orbital S2 model based on a weak overlap expansion, and the van der Waals interaction is treated in the dipolar approximation, taking into account virtual transitions of high energy. This formalism is applied here to the case of lateral interaction between CNTs, C60 dimers, adsorption of C60 on graphene and CNT, and encapsulation of C60 and CNT. The power law of the interaction is analyzed, and useful parameters such as C6 coefficients and an exponential model for the “chemical” interaction are extracted. Beyond the study of graphitic materials, this work opens interesting perspectives in the analysis of weakly bonded metal/organics interfaces.

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

2009-04-01

128

Computational studies of intermolecular interactions in aqueous solutions of poly(vinylmethylether).  

PubMed

Thermo-responsive materials, such as poly(vinylmethylether) (PVME), attract a common attention because of their unique physical properties resulted from metastable equilibrium between various types of interactions. In this work Monte Carlo (MC) and quantum-mechanical (QM) methods were used to study excluded volume and electrostatic interactions respectively. The graining procedure of PVME-water system was proposed. Its implementation to MC calculations allowed to distinguish how two water fractions differ on dynamics. The QM calculations showed that the formation of cyclic clusters leads to the lengthening of the hydrogen bonds and consequently to higher energies in comparison to linear forms, which is crucial looking at an application of QM results to MC calculation considering thermal interactions. PMID:25420704

Saramak, J; Halagan, K; Kozanecki, M; Polanowski, P

2014-12-01

129

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

130

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

131

Intradimer/Intermolecular interactions suggest autoinhibition mechanism in endophilin A1.  

PubMed

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

Chen, Zhiming; Chang, Ken; Capraro, Benjamin R; Zhu, Chen; Hsu, Chih-Jung; Baumgart, Tobias

2014-03-26

132

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

PubMed

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

Haward, Simon J

2014-01-01

133

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

PubMed Central

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

Haward, Simon J.

2014-01-01

134

DFT study on the intermolecular interactions between Au n ( n = 2–4) and thymine  

Microsoft Academic Search

The interaction between small gold clusters and thymine was studied using density functional method (DFT). Geometries of neutral thymine with Aun (n=2–4) clusters were optimized using the B3LYP method. The 6-31G+(d,p) basis set was used for thymine and the Stuttgart\\/Dresden effective core potential (ECP) basis set SDD was employed for the gold atom. Structural parameters and energy properties were discussed

Gang Lv; Fadong Wei; Hui Jiang; Yanyan Zhou; Xuemei Wang

2009-01-01

135

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

PubMed

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

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

2014-12-14

136

Tuning intermolecular interactions to enhance solid-state nanopore force spectroscopy  

NASA Astrophysics Data System (ADS)

Nanopores, nanometer sized holes in membranes, have recently come into prominence as tools for single molecule sensing. A technique called nanopore force spectroscopy uses the nanopore to probe energy landscapes between molecules. With the development of this technique, it will be possible for molecular recognition in complex fluids, such as blood. However, before that can be possible, solid-state nanopores, commonly fabricated in silicon nitride membranes, and having very confined sizes and charged surfaces, need to be optimized to minimize unwanted interactions between solution-phase molecules and the surface. DNA, for example, a crucial part of nanopore force spectroscopy, frequently sticks to the nanopore surface. Surface functionalization techniques, both on the nanopore and molecular surface, were attempted in this thesis work. These surface functionalization methods aimed to reduce surface charge or alter molecular properties in order to minimize the unwanted surface interactions, and they include silane modification, fluid lipid bilayer coating, and surfactant self-assembly on the DNA phosphate backbone. Results from some of these methods yield insights to improve nanopore force spectroscopy performance that will minimize the unwanted surface interactions and deliver on the promise of nanopore sensing.

Foun, Elaine

137

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

PubMed

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

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

2013-08-01

138

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

PubMed

This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H2O)n](m+)(H2O)? clusters (n going from 6 to 10 and ? from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R(Cf-O) in the range 2.43-2.48 Å, whereas the fourth one is closer to 9 with R(Cf-O) = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination. PMID:24907987

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

2014-06-01

139

Intermolecular C-H⋯O interactions in cyclopentanone: An inelastic neutron scattering study  

NASA Astrophysics Data System (ADS)

The inelastic neutron scattering (INS) spectra of cyclopentanone were obtained for pure and 50% CCl4 solution forms. Spectra are compared with infrared and Raman data, and with DFT calculated eigenvectors. This exercise aims to find spectroscopic evidence in the neutron spectra for the presence of C-H⋯O hydrogen bonds. These are weak interactions with an energy of ca. -6 kJ mol-1 as predicted by DFT. The neutron spectra show narrow and sharp bands which allows for an assignment of the vibrational modes. The simulated neutron spectrum of C-H⋯O bonded cyclopentanone dimers matches the experimental spectrum of the pure compound, whereas the monomer simulation monomer matches the experimental spectrum of the diluted solution, meaning that such interaction can be probed by INS. Assignment of the 95 cm-1 band to the ?H⋯O anti-translational mode, being supported by DFT results and in agreement with previous literature data, is considered and discussed.

Vaz, Pedro D.; Nolasco, Mariela M.; Ribeiro-Claro, Paulo J. A.

2013-12-01

140

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

PubMed

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

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

2013-01-15

141

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. PMID:822894

Gingell, D; Fornes, J A

1976-01-01

142

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

PubMed

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

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

2011-05-01

143

Radiative recombination of trapped excitons in Alq3 films: Importance of intermolecular interactions  

NASA Astrophysics Data System (ADS)

We investigate the light emission of optically excited tris(8-hydroxyquinolinato) aluminum (Alq3) films by temperature-dependent, time-integrated, as well as time-resolved photoluminescence (PL) at various photon densities. The Alq3 films are deposited on Si (001) substrate using organic molecular beam deposition. At high excitation densities, the PL efficiency decreases when the temperature is reduced from 170 to 15 K. At low laser intensities, the PL efficiency is nearly temperature independent. The observed PL quenching at high-excitation densities is assigned to singlet-singlet annihilation revealing a low-temperature bimolecular quenching coefficient that is more than two orders of magnitude higher than previously reported at room temperature. The observed strong bimolecular interaction at low temperature is attributed to an enhanced local (microscopic) density of captured excitons in extended traps. The reduction of the exciton annihilation with increasing temperature is assigned to a thermally activated occupation of nonquenchable localized exciton states. Above 190 K, the PL efficiency starts to decrease independently from the excitation level which is ascribed to a thermally activated detrapping of excitons and subsequent migration to nonradiative centers outside the traps. A coupled-rate equation model, including bimolecular quenching, thermally activated occupation of nonquenchable states, and detrapping of excitons at higher temperatures, supports these interpretations.

Ajward, A. M.; Wang, X.; Wickremasinghe, N.; DeSilva, L. A. A.; Wagner, H. P.

2013-07-01

144

Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach  

NASA Astrophysics Data System (ADS)

An energy decomposition scheme based on the block-localized wave function (BLW) method is proposed. The key of this scheme is the definition and the full optimization of the diabatic state wave function, where the charge transfer among interacting molecules is deactivated. The present energy decomposition (ED), BLW-ED, method is similar to the Morokuma decomposition scheme in definition of the energy terms, but differs in implementation and the computational algorithm. In addition, in the BLW-ED approach, the basis set superposition error is fully taken into account. The application of this scheme to the water dimer and the lithium cation-water clusters reveals that there is minimal charge transfer effect in hydrogen-bonded complexes. At the HF/aug-cc-PVTZ level, the electrostatic, polarization, and charge-transfer effects contribute 65%, 24%, and 11%, respectively, to the total bonding energy (-3.84 kcal/mol) in the water dimer. On the other hand, charge transfer effects are shown to be significant in Lewis acid-base complexes such as H3NSO3 and H3NBH3. In this work, the effect of basis sets used on the energy decomposition analysis is addressed and the results manifest that the present energy decomposition scheme is stable with a modest size of basis functions.

Mo, Yirong; Gao, Jiali; Peyerimhoff, Sigrid D.

2000-04-01

145

Clarification of isomeric structures and the effect of intermolecular interactions in blue-emitting aluminum complex Alq3 using first-principles 27Al NMR calculations  

NASA Astrophysics Data System (ADS)

We have performed structure analysis of the blue-emitting aluminum complex Alq3 using 27Al NMR and gauge-including projector-augmented wave calculations. The results clearly show that 27Al NMR spectra are insensitive to intermolecular interactions, thus providing a means of carrying out precise intramolecular structure determination. The key determinant of the blue-shifted emission of Alq3 is the facial isomerization.

Suzuki, Furitsu; Nishiyama, Yusuke; Kaji, Hironori

2014-06-01

146

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

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

147

The CO-Ne van der Waals complex: ab initio intermolecular potential energy, interaction induced electric dipole moment and polarizability surfaces, and second virial coefficients.  

PubMed

The intermolecular potential energy, interaction induced electric dipole moment and polarizability surfaces of the CO-Ne van der Waals complex are calculated using coupled cluster methods and the d-aug-cc-pVTZ basis set extended with a set of 3s3p2d1f1g midbond functions placed in the middle of the van der Waals bond. After fitting the interaction properties to appropriate analytical functions the surfaces are further used in semiclassical calculations of the pressure, the dielectric and the refractivity second virial coefficients of the system. The interaction potential energy surface has a single minimum (-49.9952 cm(-1)), which corresponds to R = 3.383 A and theta = 79.4 degrees. The computed dielectric second virial coefficient B(epsilon) approximately -0.27 cm(6) mol(-2) around the room temperature. PMID:19851567

Baranowska, Angelika; Fernández, Berta; Rizzo, Antonio; Jansík, Branislav

2009-11-14

148

Intermolecular interaction in an open-shell ?-bound cationic complex: IR spectrum and coupled cluster calculations for C2H2+-Ar  

NASA Astrophysics Data System (ADS)

The intermolecular potential energy surface (PES) of Ar interacting with the acetylene cation in its 2?u ground electronic state is characterized by infrared photodissociation (IRPD) spectroscopy and quantum chemical calculations. In agreement with the theoretical predictions, the rovibrational analysis of the IRPD spectrum of C2H2+-Ar recorded in the vicinity of the antisymmetric CH stretching fundamental (?3) is consistent with a vibrationally averaged T-shaped structure and a ground-state center-of-mass separation of Rc.m.=2.86±0.09 Å. The ?3 band experiences a blueshift of 16.7 cm-1 upon complexation, indicating that vibrational excitation slightly reduces the interaction strength. The two-dimensional intermolecular PES of C2H2+-Ar, obtained from coupled cluster calculations with a large basis set, features strong angular-radial coupling and supports in addition to a global ?-bound minimum also two shallow side wells with linear H-bound geometries. Bound state rovibrational energy level calculations are carried out for rotational angular momentum J=0-10 (both parities) employing a discrete variable representation-distributed Gaussian basis method. Effective spectroscopic constants are determined for the vibrational ground state by fitting the calculated rotational energies to the standard Watson A-type Hamiltonian for a slightly asymmetric prolate top.

Dopfer, Otto; Olkhov, Rouslan V.; Mladenovi?, Mirjana; Botschwina, Peter

2004-07-01

149

Intermolecular interaction in an open-shell pi-bound cationic complex: IR spectrum and coupled cluster calculations for C2H2+-Ar.  

PubMed

The intermolecular potential energy surface (PES) of Ar interacting with the acetylene cation in its (2)Pi(u) ground electronic state is characterized by infrared photodissociation (IRPD) spectroscopy and quantum chemical calculations. In agreement with the theoretical predictions, the rovibrational analysis of the IRPD spectrum of C(2)H(2) (+)-Ar recorded in the vicinity of the antisymmetric CH stretching fundamental (nu(3)) is consistent with a vibrationally averaged T-shaped structure and a ground-state center-of-mass separation of R(c.m.) = 2.86 +/- 0.09 A. The nu(3) band experiences a blueshift of 16.7 cm(-1) upon complexation, indicating that vibrational excitation slightly reduces the interaction strength. The two-dimensional intermolecular PES of C(2)H(2) (+)-Ar, obtained from coupled cluster calculations with a large basis set, features strong angular-radial coupling and supports in addition to a global pi-bound minimum also two shallow side wells with linear H-bound geometries. Bound state rovibrational energy level calculations are carried out for rotational angular momentum J = 0-10 (both parities) employing a discrete variable representation-distributed Gaussian basis method. Effective spectroscopic constants are determined for the vibrational ground state by fitting the calculated rotational energies to the standard Watson A-type Hamiltonian for a slightly asymmetric prolate top. PMID:15260724

Dopfer, Otto; Olkhov, Rouslan V; Mladenovic, Mirjana; Botschwina, Peter

2004-07-22

150

Aggregation of [Au(CN)4]- anions: examination by crystallography and 15N CP-MAS NMR and the structural factors influencing intermolecular Au···N interactions.  

PubMed

To investigate the factors influencing the formation of intermolecular Au···NC interactions between [Au(CN)(4)](-) units, a series of [cation](n+)[Au(CN)(4)](n) double salts was synthesized, structurally characterized and probed by IR and (15)N{(1)H} CP-MAS NMR spectroscopy. Thus, [(n)Bu(4)N][Au(CN)(4)], [AsPh(4)][Au(CN)(4)], [N(PPh(3))(2)][Au(CN)(4)], [Co(1,10-phenanthroline)(3)][Au(CN)(4)](2), and [Mn(2,2';6',2''-terpyridine)(2)][Au(CN)(4)](2) show [Au(CN)(4)](-) anions that are well-separated from one another; no Au-Au or Au···NC interactions are present. trans-[Co(1,2-diaminoethane)(2)Cl(2)][Au(CN)(4)] forms a supramolecular structure, where trans-[Co(en)(2)Cl(2)](+) and [Au(CN)(4)](-) ions are found in separate layers connected by Au-CN···H-N hydrogen-bonding; weak Au···NC coordinate bonds complete octahedral Au(III) centers, and support a 2-D (4,4) network motif of [Au(CN)(4)](-)-units. A similar structure-type is formed by [Co(NH(3))(6)][Au(CN)(4)](3)·(H(2)O)(4). In [Ni(1,2-diaminoethane)(3)][Au(CN)(4)](2), intermolecular Au···NC interactions facilitate formation of 1-D chains of [Au(CN)(4)](-) anions in the supramolecular structure, which are separated from one another by [Ni(en)(3)](2+) cations. In [1,4-diazabicyclo[2.2.2]octane-H][Au(CN)(4)], the monoprotonated amine cation forms a hydrogen-bond to the [Au(CN)(4)](-) unit on one side, while coordinating to the axial sites of the gold(III) center through the unprotonated amine on the other, thereby generating a 2-D (4,4) net of cations and anions; an additional, uncoordinated [Au(CN)(4)](-)-unit lies in the central space of each grid. This body of structural data indicates that cations with hydrogen-bonding groups can induce intermolecular Au···NC interactions, while the cationic charge, shape, size, and aromaticity have little effect. While the ?(CN) values are poor indicators of the presence or absence of N-cyano bridging between [Au(CN)(4)](-)-units (partly because of the very low intensity of the observed bands), (15)N{(1)H} CP-MAS NMR reveals well-defined, ordered cyanide groups in the six diamagnetic compounds with chemical shifts between 250 and 275 ppm; the resonances between 260 and 275 ppm can be assigned to C-bound terminal ligands, while those subject to CN···H-N bonding resonate lower, around 250-257 ppm. The (15)N chemical shift also correlates with the intermolecular Au···N distances: the shortest Au-N distances also shift the (15)N peak to lower frequency. This provides a real, spectroscopically measurable electronic effect associated with the crystallographic observation of intermolecular Au···NC interactions, thereby lending support for their viability. PMID:21268652

Geisheimer, Andrew R; Wren, John E C; Michaelis, Vladimir K; Kobayashi, Masayuki; Sakai, Ken; Kroeker, Scott; Leznoff, Daniel B

2011-02-21

151

Structural information from OH-stretching vibrations—XVI. On the intra- and intermolecular interactions of saturated tertiary alcohols in CCl 4 and CS 2  

NASA Astrophysics Data System (ADS)

The band parameters of the OH-stretching vibration of tertiary alcohols, including two cubylalcohols, dissolved in CCl 4 and CS 2 have been studied. The data of the strained cyclic cubylalcohols prove to be clearly different from the normal saturated tertiary alcohols. The different behaviour is related to an increased ionic character and a decreased shielding of the OH. Compared with the phenols the saturated tertiary alcohols are less sensitive to intermolecular interactions whereas the cubylalcohols behave more or less like the phenols. From the ?HBW and the ? d parameters it is concluded that local and bulk solvent interactions contribute to all band parameters. Furthermore, it is demonstrated that for the tertiary alcohols and the phenols the intramolecular effects of ortho-alkyl substitution are similar.

Lutz, E. T. G.; van der Maas, J. H.

152

An effective method for studying intermolecular interactions in binary liquids with hydrogen bonds; FTIR spectra and ab initio calculations in the N-methylformamide-methanol system.  

PubMed

Molecular complexes in methanol (MeOH)-N-methylformamide (NMF) mixtures were studied based on their FTIR-ATR spectra, to which two methods of analysis were applied: factor analysis and a quantitative version of the difference-spectra method. The mean composition of a complex between NMF and MeOH molecules over the whole range of mixture compositions was determined. Absorbing species differentiated with regard to the interaction energies of the carbonyl oxygen with methanol molecules were recognized in both compositional regions with a marked excess of one component. Possible structures for complexes of various stoichiometries were optimized by ab initio calculations in the gas phase and both liquid NMF and MeOH using the polarizable continuum model (PCM). Thermodynamic functions calculated for the optimized structures were used to find the most stable structure for each stoichiometry. Individuals distinguished by the spectral analysis were assigned to the complexes of definite composition, and a linear correlation between the positions of the carbonyl group absorption and the total interaction energies of the complexes was found. The results of the spectral analysis of the NMF-MeOH mixtures were compared to those we obtained previously for similar binary systems, i.e., mixtures of methanol and formamide (FA) or N,N-dimethylformamide (DMF). It was shown that the factor analysis applied to the infrared spectra is an effective method for distinguishing molecular complexes with different polarizations of component molecules and allows for the detection of even weak intermolecular interactions and low-concentration species. Combined with the difference-spectra method, factor analysis provides a comprehensive picture of intermolecular interactions in binary mixtures. PMID:20380396

Kamie?ska-Piotrowicz, Ewa; Dziewulska, Kamila; Stangret, Janusz

2010-05-01

153

Nuclear spin relaxation driven by intermolecular dipolar interactions: the role of solute-solvent pair correlations in the modeling of spectral density functions.  

PubMed

Nuclear spin relaxation provides useful information related to the dynamics of molecular systems. When relaxation is driven by intermolecular dipolar interactions, the relevant spectral density functions (SDFs) also have significant contributions, in principle, from distant spins all over the dynamic range typically probed by NMR experiments such as NOESY. In this work, we investigate the intermolecular dipolar spin relaxation as driven by the relative diffusion of solvent and solute molecules taking place under a central force field, and we examine the relevant implications for (preferential) solvation studies. For this purpose, we evaluate the SDFs by employing a numerical approach based on spatial discretization of the time-propagation equation, and we supply an analytical solution for the simplest case of a steplike mean-field potential. Several situations related to different solute-solvent pair correlation functions are examined in terms of static/dynamic effects and relaxation modes, and some conclusions are drawn about the interpretation of NOE measurements. While we confirm previous results concerning the spoiling effect of long-range spins (Halle, B. J. Chem. Phys. 2003, 119, 12372), we also show that SDFs are sufficiently sensitive to pair correlation functions that useful, yet rather complicated, inferences can be made on the nature of the solvation shell. PMID:16539513

Frezzato, Diego; Rastrelli, Federico; Bagno, Alessandro

2006-03-23

154

Small and efficient basis sets for the evaluation of accurate interaction energies: aromatic molecule-argon ground-state intermolecular potentials and rovibrational States.  

PubMed

By evaluating a representative set of CCSD(T) ground state interaction energies for van der Waals dimers formed by aromatic molecules and the argon atom, we test the performance of the polarized basis sets of Sadlej et al. (J. Comput. Chem. 2005, 26, 145; Collect. Czech. Chem. Commun. 1988, 53, 1995) and the augmented polarization-consistent bases of Jensen (J. Chem. Phys. 2002, 117, 9234) in providing accurate intermolecular potentials for the benzene-, naphthalene-, and anthracene-argon complexes. The basis sets are extended by addition of midbond functions. As reference we consider CCSD(T) results obtained with Dunning's bases. For the benzene complex a systematic basis set study resulted in the selection of the (Z)Pol-33211 and the aug-pc-1-33321 bases to obtain the intermolecular potential energy surface. The interaction energy values and the shape of the CCSD(T)/(Z)Pol-33211 calculated potential are very close to the best available CCSD(T)/aug-cc-pVTZ-33211 potential with the former basis set being considerably smaller. The corresponding differences for the CCSD(T)/aug-pc-1-33321 potential are larger. In the case of the naphthalene-argon complex, following a similar study, we selected the (Z)Pol-3322 and aug-pc-1-333221 bases. The potentials show four symmetric absolute minima with energies of -483.2 cm(-1) for the (Z)Pol-3322 and -486.7 cm(-1) for the aug-pc-1-333221 basis set. To further check the performance of the selected basis sets, we evaluate intermolecular bound states of the complexes. The differences between calculated vibrational levels using the CCSD(T)/(Z)Pol-33211 and CCSD(T)/aug-cc-pVTZ-33211 benzene-argon potentials are small and for the lowest energy levels do not exceed 0.70 cm(-1). Such differences are substantially larger for the CCSD(T)/aug-pc-1-33321 calculated potential. For naphthalene-argon, bound state calculations demonstrate that the (Z)Pol-3322 and aug-pc-1-333221 potentials are of similar quality. The results show that these surfaces differ substantially from the available MP2/aug-cc-pVDZ potential. For the anthracene-argon complex it proved advantageous to calculate interaction energies by using the (Z)Pol and the aug-pc-1 basis sets, and we expect it to be increasingly so for complexes containing larger aromatic molecules. PMID:25317989

Cybulski, Hubert; Baranowska-??czkowska, Angelika; Henriksen, Christian; Fernández, Berta

2014-11-01

155

Synthesis, tautomeric forms, specific intermolecular interactions, and lipophilicity of methylated 6-hydroxypyridazine-3-carboxylic acid and its 4,5-dihydro analogs  

NASA Astrophysics Data System (ADS)

Effects of methylation for intermolecular interactions and lipophilicity have been studied for a series of methylated 4,5-dihydro-6-hydroxypyridazine-3-carboxylic and 6-hydroxypyridazine-3-carboxylic acids ( 1 and 2). In solution they exist in equilibrium of the lactam and lactim tautomers, with the reverse preferences for analogs 1 and 2, which affect the syntheses of their methylated derivatives. Carboxylic acid 2 preferably crystallizes as a hydrate, built of carboxylate anions and hydronium cations 2- rad H 3O +, hydrogen bonded into catemeric patterns involving both ions. In methyl 4,5-dihydro-6-oxopyridazine-3-carboxylate ( 4A) the molecules are NH⋯O hydrogen bonded into chains. In both structures 2- rad H 3O + and 4A, there are relatively strong CH⋯O hydrogen bonds, arranging the molecules into sheets. The increased lipophilicity of the methylated derivatives has been correlated with the formation of CH⋯O bonds.

Katrusiak, Anna; Piechowiak, Pawe?; Katrusiak, Andrzej

2011-07-01

156

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

SciTech Connect

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

Xantheas, Sotiris S.; Werhahn, Jasper C.

2014-08-14

157

In-vitro anti-proliferative and anti-oxidant activity of galangin, fisetin and quercetin: role of localization and intermolecular interaction in model membrane.  

PubMed

Flavonols are an important class of naturally occurring molecules and are known for their pharmacological activity. The activity is associated with the ability of flavonols to influence membrane-dependent processes. We have investigated the in-vitro anti-proliferative and anti-oxidant activity of galangin (GLN), fisetin (FTN) and quercetin (QTN), which possess variable number of phenolic hydroxyl groups. An attempt has been made to correlate the biological activity of these molecules with their interaction and localization in dipalmitoyl phosphatidyl choline (DPPC) bilayers, using differential dcanning calorimetry (DSC) and nuclear magnetic resonance (NMR) methods. Results indicate that GLN interacts to the alkyl chains of the lipid bilayer involving hydrophobic interactions. FTN and QTN interact with head region and sn-1-glycero region involving hydrogen bonding. Ring current induced chemical shifts of lipid protons, due to intermolecular interaction indicate that GLN acquires a parallel orientation with respect to the bilayer normal whereas FTN and QTN resume a mixed orientation. The membrane binding constants of these molecules are in the order GLN > QTN > FTN. It has been shown that the number and position of hydroxyl groups in these molecules play an important role in membrane binding and thereby in biological activity. PMID:24727463

Sinha, Ragini; Srivastava, Sudha; Joshi, Akshada; Joshi, Urmila J; Govil, Girjesh

2014-05-22

158

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. PMID:24116125

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

2013-01-01

159

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. PMID:17580120

Kheifets, Viktoria; Mochly-Rosen, Daria

2007-01-01

160

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

NASA Astrophysics Data System (ADS)

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

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

2006-09-01

161

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

NASA Astrophysics Data System (ADS)

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

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

2010-04-01

162

Surface activity at the planar interface in relation to the thermodynamics of intermolecular interactions in the ternary system: maltodextrin-small-molecule surfactant-legumin.  

PubMed

We report on the effect of potato maltodextrins with variable dextrose equivalent (Paselli SA-2, SA-6 and SA-10) on the surface behavior at the air-water interface of the mixture: legumin+small-molecule surfactant. Distinct in nature small-molecule surfactants (model: sodium salt of capric acid, Na-caprate; and commercially important: a citric acid ester of monoglyceride, CITREM) have been under our consideration. The role of the structure of both of the maltodextrins and the small-molecule surfactants in the effect studied has been elucidated by measurements in a bulk aqueous medium of the enthalpy of their interaction from mixing calorimetry, value of weight average molecular weight of the maltodextrins and the thermodynamics of the pair maltodextrin-solvent and maltodextrin-protein interactions from laser static light scattering. The combined data of mixing calorimetry and light scattering suggest some complex formation between the small-molecule surfactants and the maltodextrins. Predominantly hydrophobic interactions along with hydrogen bonding form the basis of the complexes. The effect of the maltodextrins on the thermodynamics of the protein heat denaturation and thereby on the protein conformational stability in the presence of the small-molecule surfactants has been studied by differential scanning calorimetry. The interrelation between the thermodynamics of intermolecular interactions in a bulk and the surface behavior at the planar air-water interface of the ternary systems (maltodextrin+legumin+small-molecule surfactant) has been elucidated by tensiometry. The effect of the maltodextrins on the surface activity of mixtures of legumin with the small-molecule surfactants is governed by the competitive in relation to the protein interactions with the small-molecule surfactants and a subsequent change in the thermodynamic properties of the both biopolymers, which are favorable to the ternary complex formation. PMID:11377947

Myasoedova, M S.; Semenova, M G.; Belyakova, L E.; Antipova, A S.

2001-07-01

163

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

164

Phase separation in an exactly solvable model binary solution with three-body interactions and intermolecular bonding  

Microsoft Academic Search

A model is presented in which the bonds of a honeycomb lattice are covered by rodlike molecules of types AA and BB , molecular ends near a common site having both three-body interactions and orientation-dependent bonding between two A molecular ends and between an A and a B molecular end. Phase diagrams corresponding to the separation into AA -rich and

Radu P. Lungu; Dale A. Huckaby; Florin D. Buzatu

2006-01-01

165

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

NASA Astrophysics Data System (ADS)

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

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

2009-08-01

166

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

SciTech Connect

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

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

2013-08-29

167

Direct Calculation of the Intermolecular Interaction Potential from the Extended Principle of Corresponding States for N2-He  

NASA Astrophysics Data System (ADS)

An inversion procedure is used to obtain the interaction potential from the extended principle of corresponding states. Over a range of reduced temperature extending from 1 to 100 this directly calculated potential for N2-He agrees excellently with the ESMSV-type independently known potential. This accurate inverted potential can be used to obtain the orientation averaged viscosity collision integrals and the dimensionless ratios that are essential to calculate other transport properties.

Najafi, Mohsen; Haghighi, Behzad

2000-01-01

168

Relationships between interaction energy, intermolecular distance and electron density properties in hydrogen bonded complexes under external electric fields  

NASA Astrophysics Data System (ADS)

The hydrogen bond interaction energy (EHB) of HF⋯HR (R = H, Li, Al, Cl, CCH) complexes under external electric fields is investigated in terms of the bonding distance and of several properties at the bond critical point. All these properties can be used for the estimation of EHB, being the positive curvature along the hydrogen bond path the most suited for the application to experimental electron densities.

Mata, I.; Alkorta, I.; Espinosa, E.; Molins, E.

2011-04-01

169

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

SciTech Connect

This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H{sub 2}O){sub n}]{sup m+}(H{sub 2}O){sub ?} clusters (n going from 6 to 10 and ? from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H{sub 2}O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R{sub Cf??O} in the range 2.43–2.48 Å, whereas the fourth one is closer to 9 with R{sub Cf??O} = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.

Galbis, Elsa; Pappalardo, Rafael R.; Marcos, Enrique Sánchez, E-mail: sanchez@us.es [Departmento de Química Física, Universidad de Sevilla, 41012 Seville (Spain); Hernández-Cobos, Jorge [Instituto de Ciencias Físicas, UNAM, Apartado Postal 48-3, 62251 Cuernavaca (Mexico)

2014-06-07

170

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

NASA Astrophysics Data System (ADS)

This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H2O)n]m+(H2O)? clusters (n going from 6 to 10 and ? from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R_{{Cf-O}} in the range 2.43-2.48 Å, whereas the fourth one is closer to 9 with R_{{Cf-O}} = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.

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

2014-06-01

171

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

172

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

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

173

Intra- and intermolecular interactions in the crystals of 3,4-diamino-1,2,4-triazole and its 5-methyl derivative. Experimental and theoretical investigations of charge density distribution.  

PubMed

In this paper intra- and intermolecular interactions in crystals of 3,4-diamino-1,2,4-triazole (DAT) and its 5-methyl derivative (DAMT) were investigated in details by experimental (high-resolution X-ray diffraction) and theoretical (ab initio quantum chemistry (MP2/aug-cc-pvdz), AIM, and NBO) methods. Influence of n-? conjugation and n??* hyperconjugation on the geometry of DAT and DAMT molecules was shown. All intermolecular interactions in crystals of the DAT and DAMT including weak X-H···? and mixed X-H···N/X-H···? hydrogen bonds were considered. Comparison of BCP characteristics of these interactions from experimental and theoretical charge density distribution demonstrates systematic increase of bonding in isolated dimers compared with dimers in the crystal phase. The ability of amino groups in both crystals serve as proton acceptors in hydrogen bonding was confirmed. PMID:21678964

Konovalova, Irina S; Nelyubina, Yuliya V; Lyssenko, Konstantin A; Paponov, Boris V; Shishkin, Oleg V

2011-08-01

174

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

NASA Astrophysics Data System (ADS)

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

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

2008-05-01

175

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

PubMed

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

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

2014-08-25

176

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

NASA Astrophysics Data System (ADS)

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

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

2010-08-01

177

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

PubMed

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

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

2014-12-30

178

Heterometallic complexes with gold(i) metalloligands: self-assembly of helical dimers stabilized by weak intermolecular interactions and solvophobic effects.  

PubMed

New gold(I) alkynyl metalloligands bpylC?CAuL, bpyl'C?CAuPPh3 , and PPN[Au(C?Cbpyl')2 ] (bpyl or bpyl'=2,2'-bipyridin-5-yl or -4-yl, respectively; L=PMex Ph3-x (x=1-3), P(C6 H3 Me2 -3,5)3 , PCy3 , XyNC) have been synthesized. Ligands bpylC?CH and metalloligands bpylC?CAuL (L=PPh3 , PMePh2 , PCy3 , CNXy) react with MX2 (M=Fe, Zn, X=ClO4 ; M=Co, X=BF4 ) to give complexes [M(bpylC?CZ)3 ]X2 (Z=H or AuL). In most cases, these complexes are mixtures of fac and mer isomers in a statistical distribution, in both CH2 Cl2 and MeCN. However, for L=PPh3 , the fac isomer is dominant in MeCN. NMR and ESI-MS studies, together with the crystal structure of [Co(bpylC?CAuPPh3 )3 ](BF4 )2 , suggest that this solvent dependence is originated by the formation of helical dimers between two fac complexes in MeCN. These dimers are stabilized by solvophobic effects and multiple intermolecular interactions. Complex [Fe(Ph3 PAuC?CbpdiylC?CAuPPh3 )3 ](ClO4 )2 (bpdiyl=2,2'-bipyridin-5,5'-diyl) was obtained by reaction of three diauro diethynylbipyridines and Fe(ClO4 )2 . PMID:25469496

Cámara, Verónica; Barquero, Natalia; Bautista, Delia; Gil-Rubio, Juan; Vicente, José

2015-01-26

179

Analysis of radiatively stable entanglement in a system of two dipole-interacting three-level atoms  

E-print Network

three-level dipole- interacting atoms in a configuration by means of laser biharmonic continuous driving proposed and some of them experimentally demonstrated 12,13 . Though the resonant dipole-dipole interaction at a distance R. The dipole transitions 1 3 and 2 3 of both atoms are driven by two near-resonant laser fields

Zadkov, Victor

180

FT-IR study on interactions between medroxyprogesterone acetate and solvent in CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 binary solvent systems  

NASA Astrophysics Data System (ADS)

The intermolecular interactions between medroxyprogesterone acetate (MPA) and CHCl3 and CCl4 solvent in CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 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 CHCl3 so as to form 1:3 complex of MPA with CHCl3 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 CCl4 is formed in CCl4/cyclo-C6H12 binary solvent as a result of hydrogen bonding interaction between C3 carbonyl group and empty d-orbital in chlorine atom of CCl4 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 CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 binary solvent systems shift to lower wavenumbers with the increasing of volume fraction of CHCl3 and CCl4 in binary solvent systems owing to the dipole-dipole interaction and the dipole-induced dipole interaction between MPA and solvents.

Shi, Jie-hua; Fan, Chun-hui

2012-09-01

181

Competing interactions in semiconductor quantum dots  

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

182

Calculating intermolecular potentials with SIMPER: the water–nitrogen and water–oxygen interactions, dispersion energy coefficients, and preliminary results for larger molecules  

Microsoft Academic Search

Recent theoretical studies of the van der Waals complexes formed between water and the two main components of air, nitrogen and oxygen, are reviewed. Combined with previous work on the water–argon complex, the results allow non-ideal thermodynamic properties of water–air mixtures to be calculated. The intermolecular potential energy surfaces for these complexes have been calculated using a combination of supermolecule

Richard J. Wheatley; Timothy C. Lillestolen

2007-01-01

183

Electrostatic interactions in computer simulations of a three-dimensional system periodic in two directions: Ewald-type summation  

NASA Astrophysics Data System (ADS)

We show analytically that the two-dimensional Ewald summation of the Coulomb and dipole-dipole interaction energy may be approximated by the conventional three-dimensional Ewald method. However, an empty space must be introduced in the simulation box, and

Brodka, A.; Grzybowski, A.

2002-11-01

184

Anisotropy in the Interaction of Ultracold Dysprosium  

E-print Network

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 L=6 and magnetic moment $\\mu=10\\mu_B$. 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 $R< 50\\,a_0$ 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 spin exchange can occur. We finish by describing two scattering models for inelastic spin exchange. A universal scattering theory is used to model loss due to the anisotropy in the dispersion and a distorted-wave-Born theory is used to model losses from the magnetic dipole-dipole interaction for the $^{164}$Dy isotope. These models find loss rates that are the same order of magnitude as the experimental value.

Svetlana Kotochigova; Alexander Petrov

2011-04-28

185

Intermolecular Forces: A Jigsaw Activity  

NSDL National Science Digital Library

This jigsaw activity is designed as a cooperative learning activity used to introduce the idea of intermolecular forces. Intermolecular forces are the types of attractive forces that occur between molecules in a solid, liquid, or gas. Each force causes different physical properties of matter. Each member of the group will become an expert on one type of force and then teach the rest of the group.

Edu., Boise S.

2011-09-20

186

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

PubMed

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

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

1989-08-15

187

Poly[(?-pentafluorobenzoato-?²O:O')(pentafluorobenzoato-?O)(?-pyrazine-?²N:N')copper(II)]: a coordination polymer linked into a three-dimensional network by intermolecular C-H···F-C interactions.  

PubMed

In the title compound, [Cu(C6F5COO)2(C4H4N2)]n, (I), the asymmetric unit contains one Cu(II) cation, two anionic pentafluorobenzoate ligands and one pyrazine ligand. Each Cu(II) centre is five-coordinated by three O atoms from three independent pentafluorobenzoate anions, as well as by two N atoms from two pyrazine ligands, giving rise to an approximately square-pyramidal coordination geometry. Adjacent Cu(II) cations are bridged by a pyrazine ligand and two pentafluorobenzoate anions to give a two-dimensional layer. The layers are stacked to generate a three-dimensional supramolecular architecture via strong intermolecular C-H···F-C interactions, as indicated by the F···H distance of 2.38?Å. PMID:25370097

Han, Li-Juan; Kong, Ya-Jie

2014-11-01

188

Intermolecular Adhesion in Conjugated Polymers  

E-print Network

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

Jeremy D. Schmit; Alex J. Levine

2006-10-25

189

A study for the cause of ferulic acid-induced quenching of tyrosine fluorescence and whether it is a reliable marker of intermolecular interactions or not.  

PubMed

Intrinsic fluorescence of peptides and proteins is extensively used to monitor their specific interactions with several natural and synthetic molecules known to have wide-ranging beneficial or detrimental effects on health. A consequence of these interactions would be a significant decrease of the fluorescence emission intensity of Tyrosine (Tyr) and/or Tryptophan (Trp) residues in the protein due to structural rearrangements of proteic microenvironment. However fluorescence quenching can be also caused by "trivial" artefacts. In this study we examined the effect of Ferulic acid (FA) on Tyr fluorescence. FA is a natural anti-oxidant suggested to bind to and to modify the structural properties of several proteins thus altering their biological activities. Fluorescence spectroscopy experiments on Tyr and on proteins containing Tyr and no Trp like beta amyloid peptides and Insulin were performed. Our results suggest that Tyr fluorescence loss can mainly result from an inner filter effect rather than from specific interactions with FA. PMID:23463293

Sgarbossa, Antonella; Lenci, Francesco

2013-05-01

190

Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density  

PubMed Central

A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-d-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program topxd and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP/6–31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l = 4) is found to be within 2–3 kJ/mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules. PMID:12221293

Li, Xue; Wu, Guang; Abramov, Yuriy A.; Volkov, Anatoliy V.; Coppens, Philip

2002-01-01

191

Characterization of the structure and intermolecular interactions between the connexin40 and connexin43 carboxyl-terminal and cytoplasmic loop domains.  

PubMed

Gap junctions are intercellular channels that allow the passage of ions, small molecules, and second messengers that are essential for the coordination of cellular function. They are formed by two hemichannels, each constituted by the oligomerization of six connexins (Cx). Among the 21 different human Cx isoforms, studies have suggested that in the heart, Cx40 and Cx43 can oligomerize to form heteromeric hemichannels. The mechanism of heteromeric channel regulation has not been clearly defined. Tissue ischemia leads to intracellular acidification and closure of Cx43 and Cx40 homomeric channels. However, coexpression of Cx40 and Cx43 in Xenopus oocytes enhances the pH sensitivity of the channel. This phenomenon requires the carboxyl-terminal (CT) part of both connexins. In this study we used different biophysical methods to determine the structure of the Cx40CT and characterize the Cx40CT/Cx43CT interaction. Our results revealed that the Cx40CT is an intrinsically disordered protein similar to the Cx43CT and that the Cx40CT and Cx43CT can interact. Additionally, we have identified an interaction between the Cx40CT and the cytoplasmic loop of Cx40 as well as between the Cx40CT and the cytoplasmic loop of Cx43 (and vice versa). Our studies support the "particle-receptor" model for pH gating of Cx40 and Cx43 gap junction channels and suggest that interactions between cytoplasmic regulatory domains (both homo- and hetero-connexin) could be important for the regulation of heteromeric channels. PMID:19808665

Bouvier, Denis; Spagnol, Gaelle; Chenavas, Sylvie; Kieken, Fabien; Vitrac, Heidi; Brownell, Sarah; Kellezi, Admir; Forge, Vincent; Sorgen, Paul L

2009-12-01

192

Characterization of the Structure and Intermolecular Interactions between the Connexin40 and Connexin43 Carboxyl-terminal and Cytoplasmic Loop Domains*  

PubMed Central

Gap junctions are intercellular channels that allow the passage of ions, small molecules, and second messengers that are essential for the coordination of cellular function. They are formed by two hemichannels, each constituted by the oligomerization of six connexins (Cx). Among the 21 different human Cx isoforms, studies have suggested that in the heart, Cx40 and Cx43 can oligomerize to form heteromeric hemichannels. The mechanism of heteromeric channel regulation has not been clearly defined. Tissue ischemia leads to intracellular acidification and closure of Cx43 and Cx40 homomeric channels. However, coexpression of Cx40 and Cx43 in Xenopus oocytes enhances the pH sensitivity of the channel. This phenomenon requires the carboxyl-terminal (CT) part of both connexins. In this study we used different biophysical methods to determine the structure of the Cx40CT and characterize the Cx40CT/Cx43CT interaction. Our results revealed that the Cx40CT is an intrinsically disordered protein similar to the Cx43CT and that the Cx40CT and Cx43CT can interact. Additionally, we have identified an interaction between the Cx40CT and the cytoplasmic loop of Cx40 as well as between the Cx40CT and the cytoplasmic loop of Cx43 (and vice versa). Our studies support the “particle-receptor” model for pH gating of Cx40 and Cx43 gap junction channels and suggest that interactions between cytoplasmic regulatory domains (both homo- and hetero-connexin) could be important for the regulation of heteromeric channels. PMID:19808665

Bouvier, Denis; Spagnol, Gaelle; Chenavas, Sylvie; Kieken, Fabien; Vitrac, Heidi; Brownell, Sarah; Kellezi, Admir; Forge, Vincent; Sorgen, Paul L.

2009-01-01

193

Wigner-localized states in spin-orbit-coupled bosonic ultracold atoms with dipolar interaction  

E-print Network

We investigate the occurence of Wigner-localization phenomena in bosonic dipolar ultracold few-body systems with Rashba-like spin-orbit coupling. We show that the latter strongly enhances the effects of the dipole-dipole interactions, allowing to reach the Wigner-localized regime for strengths of the dipole moment much smaller than those necessary in the spin-orbit-free case.

Yousefi, Y; Malet, F; Cremon, J; Reimann, S M

2014-01-01

194

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

195

New insights into intra- and intermolecular interactions of immunoglobulins: crystal structure of mouse IgG2b-Fc at 2·1-Å resolution  

PubMed Central

The structure of the Fc fragment of monoclonal antibody IgG2b from hybridom M75 of Mus musculus has been determined by single crystal X-ray diffraction. This is the first report of the structure of the murine immunoglobulin isotype IgG2b. The structure refined at 2·1 Å resolution provides more detailed structural information about native oligosaccharides than was previously available. High-quality Fourier maps provide a clear identification of ?-l-fucose with partial occupancy in the first branch of the antennary oligosaccharides. A unique Fc:Fc interaction was observed at the CH2-CH3 interface. PMID:18783468

Kolenko, Petr; Dohnálek, Jan; Dušková, Jarmila; Skálová, Tereza; Collard, Renata; Hašek, Jind?ich

2009-01-01

196

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

197

Proton spin dynamics in polymer melts: new perspectives for experimental investigations of polymer dynamics  

E-print Network

Significant progress was made in recent years in the understanding of the proton spin kinetics in polymer melts. Generally, the proton spin kinetics is determined by intramolecular and intermolecular magnetic dipole-dipole contributions of proton spins. During many decades it was postulated that the main contribution is a result of intramolecular magnetic dipole-dipole interactions of protons belonging to the same polymer segment. It appears that this postulate is far from reality. The relative weights of intra- and intermolecular contributions are time dependent and sensitive to details of polymer chain dynamics. It is shown that for isotropic models of polymer dynamics the influence of the intermolecular magnetic dipole-dipole interactions increases faster with increasing evolution time (i.e. decreasing frequency) than the corresponding influence of the intramolecular counterpart. On the other hand, an inverted situation is predicted by the tube-reptation model: here the influence of the intramolecular magnetic dipole-dipole interactions increases faster with time than the contribution from intermolecular interactions. The intermolecular contribution in the proton relaxation of polymer melts can experimentally be isolated using the isotope dilution technique and this opens a new perspective for experimental investigations of polymer dynamics by proton NMR.

N. Fatkullin; S. Stapf; M. Hofmann; R. Meierc; E. A. Roessler

2014-05-25

198

A quantum mechanical study of water adsorption on the (110) surfaces of rutile SnO? and TiO?: investigating the effects of intermolecular interactions using hybrid-exchange density functional theory.  

PubMed

Periodic hybrid-exchange density functional theory calculations are used to explore the first layer of water at model oxide surfaces, which is an important step for understanding the photocatalytic reactions involved in solar water splitting. By comparing the structure and properties of SnO2(110) and TiO2(110) surfaces in contact with water, the effects of structural and electronic differences on the water chemistry are examined. The dissociative adsorption mode at low coverage (1/7 ML) up to monolayer coverage (1 ML) on both SnO2 and TiO2(110) surfaces is analysed. To investigate further the intermolecular interactions between adjacent adsorbates, monolayer adsorption on each surface is explored in terms of binding energies and bond lengths. Analysis of the water adsorption geometry and energetics shows that the relative stability of water adsorption on SnO2(110) is governed largely by the strength of the chemisorption and hydrogen bonds at the surface of the adsorbate-substrate system. However on TiO2(110), a more complicated scenario of the first layer of water on its surface arises in which there is an interplay between chemisorption, hydrogen bonding and adsorbate-induced atomic displacements in the surface. Furthermore the projected density of states of each surface in contact with a mixture of adsorbed water molecules and adsorbed hydroxyls is presented and sheds some light on the nature of the crystalline chemical bonds as well as on why adsorbed water has often been reported to be unstable on rutile SnO2(110). PMID:24979063

Patel, M; Sanches, F F; Mallia, G; Harrison, N M

2014-10-21

199

Collective many-body interaction in Rydberg dressed atoms  

E-print Network

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/van der Waals Blockade phenomenon between the Rydberg levels plays a dominant role. We study the influence of these collective interaction potential on a Bose-Einstein condensate, and present the optimal parameters for its experimental detection.

Jens Honer; Hendrik Weimer; Tilman Pfau; Hans Peter Büchler

2010-04-14

200

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

201

?-Stacking, C-H/?, and halogen bonding interactions in bromobenzene and mixed bromobenzene-benzene clusters.  

PubMed

Noncovalent interactions play an important role in many chemical and biochemical processes. Building upon our recent study of the homoclusters of chlorobenzene, where ?-? stacking and CH/? interactions were identified as the most important binding motifs, in this work we present a study of bromobenzene (PhBr) and mixed bromobenzene-benzene clusters. Electronic spectra in the region of the PhBr monomer S0-S1 (??*) transition were obtained using resonant two-photon ionization (R2PI) methods combined with time-of-flight mass analysis. As previously found for related systems, the PhBr cluster spectra show a broad feature whose center is red-shifted from the monomer absorption, and electronic structure calculations indicate the presence of multiple isomers and Franck-Condon activity in low-frequency intermolecular modes. Calculations at the M06-2X/aug-cc-pVDZ level find in total eight minimum energy structures for the PhBr dimer: four ?-stacked structures differing in the relative orientation of the Br atoms (denoted D1-D4), one T-shaped structure (D5), and three halogen bonded structures (D6-D8). The calculated binding energies of these complexes, corrected for basis set superposition error (BSSE) and zero-point energy (ZPE), are in the range of -6 to -24 kJ/mol. Time-dependent density functional theory (TDDFT) calculations predict that these isomers absorb over a range that is roughly consistent with the breadth of the experimental spectrum. To examine the influence of dipole-dipole interaction, R2PI spectra were also obtained for the mixed PhBr···benzene dimer, where the spectral congestion is reduced and clear vibrational structure is observed. This structure is well-simulated by Franck-Condon calculations that incorporate the lowest frequency intermolecular modes. Calculations find four minimum energy structures for the mixed dimer and predict that the binding energy of the global minimum is reduced by ~30% relative to the global minimum PhBr dimer structure. PMID:23978255

Reid, Scott A; Nyambo, Silver; Muzangwa, Lloyd; Uhler, Brandon

2013-12-19

202

Intermolecular domain docking in the hairpin ribozyme  

PubMed Central

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

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

2013-01-01

203

Competing intramolecular vs. intermolecular hydrogen bonds in solution.  

PubMed

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

Nagy, Peter I

2014-01-01

204

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution  

PubMed Central

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

Nagy, Peter I.

2014-01-01

205

Supersolid phase in atomic gases with magnetic dipole interaction  

SciTech Connect

A major obstacle for the experimental realization of a supersolid phase with cold atomic gases in an optical lattice is the weakness of the nearest-neighbor interactions achievable via magnetic dipole-dipole interactions. In this paper, we show that by using a large filling of atoms within each well, the characteristic energy scales are strongly enhanced. Within this regime, the system is well described by the rotor model, and the qualitative behavior of the phase diagram derives from mean-field theory. We find a stable supersolid phase for realistic parameters with chromium atoms.

Buehler, Adam; Buechler, Hans Peter [Institute for Theoretical Physics III, University of Stuttgart, Pfaffenwaldring 57, D-70550 (Germany)

2011-08-15

206

Intramolecular chalcogen-tin interactions in [(o-MeEC6H4)CH2]2SnPh(2-n)Cl(n) (E = S, O, CH2; n = 0, 1, 2) and intermolecular chlorine-tin interactions in the meta- and para-methoxy isomers.  

PubMed

Organotin(IV) compounds of the type [(o-MeEC(6)H(4))CH(2)](2)SnPh(2-n)Cl(n) were synthesized, E = O, n = 0 (1), n = 1 (2), and n = 2 (3); E = S, n = 0 (4), n = 1 (5), and n = 2 (6); and E = CH(2), n = 0 (7), n = 1 (8), and n = 2 (9). The dichloro compounds 3 and 6 have been investigated by single-crystal X-ray diffraction and exhibit bicapped tetrahedral geometry at the tin atom as a consequence of significant intramolecular Sn...O (3) and Sn...S (6) secondary bonding, in monomolecular units. Compound 3, when crystallized from a hexane/THF solvent mixture, shows two different conformers, 3' and 3'', in the crystal structure; 3' has two equivalent Sn...O interactions, while 3'' has two nonequivalent Sn...O interactions. Upon the recrystallization of 3 from hexane, only a single structural form is observed, 3'. The Sn...E distances in 3', 3'', and 6 are 71.3, 73.5 and 72.9, and 76.3% of the SigmavdW radii, respectively. The meta- and para-substituted isomers of 3 (10, 11) exhibit a distortion at the tin atom due to self-association via intermolecular Sn...Cl interactions, resulting in polymeric structures. (119)Sn NMR spectroscopy suggests that the intramolecular Sn...E interactions persist in solution for the dichloride compounds 3 and 6. PMID:20047301

Vargas-Pineda, Diana Gabriela; Guardado, Tanya; Cervantes-Lee, Francisco; Metta-Magana, Alejandro J; Pannell, Keith H

2010-02-01

207

Anisotropy in the Interaction of Ultracold Dysprosium  

E-print Network

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 L=6 and magnetic moment $\\mu=10\\mu_B$. 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 $R< 50\\,a_0$ 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 ...

Kotochigova, Svetlana

2011-01-01

208

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity  

NASA Astrophysics Data System (ADS)

This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine ?-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 105 M-1] is similar to the value for the PA [(3.8 ± 0.1) × 105 M-1]; Ka for 3-OHPA [(1.1 ± 0.3) × 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

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

2014-05-01

209

Long-range Rydberg-Rydberg interactions in calcium, strontium and ytterbium  

E-print Network

Long-range dipole-dipole and quadrupole-quadrupole interactions between pairs of Rydberg atoms are calculated perturbatively for calcium, strontium and ytterbium within the Coulomb approximation. Quantum defects, obtained by fitting existing laser spectroscopic data, are provided for all $S$, $P$, $D$ and $F$ series of strontium and for the $^3P_2$ series of calcium. The results show qualitative differences with the alkali metal atoms, including isotropically attractive interactions of the strontium $^1S_0$ states and a greater rarity of F\\"orster resonances. Only two such resonances are identified, both in triplet series of strontium. The angular dependence of the long range interaction is briefly discussed.

C. L. Vaillant; M. P. A. Jones; R. M. Potvliege

2012-03-16

210

Long-range Rydberg-Rydberg interactions in calcium, strontium and ytterbium  

E-print Network

Long-range dipole-dipole and quadrupole-quadrupole interactions between pairs of Rydberg atoms are calculated perturbatively for calcium, strontium and ytterbium within the Coulomb approximation. Quantum defects, obtained by fitting existing laser spectroscopic data, are provided for all $S$, $P$, $D$ and $F$ series of strontium and for the $^3P_2$ series of calcium. The results show qualitative differences with the alkali metal atoms, including isotropically attractive interactions of the strontium $^1S_0$ states and a greater rarity of F\\"orster resonances. Only two such resonances are identified, both in triplet series of strontium. The angular dependence of the long range interaction is briefly discussed.

Vaillant, C L; Potvliege, R M

2012-01-01

211

Charge oscillations and interaction between potassium adatoms on graphene studied by first-principles calculations  

NASA Astrophysics Data System (ADS)

Interaction between K adatoms on graphene is investigated by first-principles calculations based on density function theory and analytical analyses based on the k .p perturbation theory. The calculation shows that there is a strong repulsion between K adatoms. The main origin of this strong repulsion is not from the dipole-dipole interaction as suggested for K adatoms on graphite surface, but comes from the screened Coulomb interaction. Potassium adatom on graphene donates its s electron and becomes K+. The positively charged K adatom induces electron density oscillation on graphene which is responsible for the screened Coulomb repulsion between the K adatoms.

Liu, Xiaojie; Wang, Cai-Zhuang; Lin, Hai-Qing; Chang, Kai; Chen, Jian; Ho, Kai-Ming

2015-01-01

212

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO(2) bond upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of nitrotriazole or its methyl derivatives.  

PubMed

The changes of bond dissociation energy (BDE) in the C-NO(2) bond and nitro group charge upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C-NO(2) bond was enhanced and the charge of nitro group turned more negative in complex in comparison with those in isolated nitrotriazole molecule. The increment of the C-NO(2) bond dissociation energies correlated well with the intermolecular H-bonding interaction energies. Electron density shifts analyses showed that the electron density shifted toward the C-NO(2) bond upon complex formation, leading to the strengthened C-NO(2) bond and the possibly reduced explosive sensitivity. PMID:22955424

Li, Bao-Hui; Shi, Wen-Jing; Ren, Fu-de; Wang, Yong

2013-02-01

213

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

NASA Astrophysics Data System (ADS)

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

Zhang, Peng; Jie, Jianwen

2014-12-01

214

An improved intermolecular potential for sulfur hexafluoride  

SciTech Connect

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

Aziz, R.A.; Slaman, M.J. (Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1 (US)); Taylor, W.L.; Hurly, J.J. (EG G Mound Applied Technologies, Inc., Miamisburg, Ohio 45343 (US) Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221 (US))

1991-01-15

215

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

216

Effect of intermolecular hydrogen bonding and proton transfer on fluorescence of salicylic acid  

NASA Astrophysics Data System (ADS)

Effects of intermolecular interactions, in particular the influence of intermolecular hydrogen bonds formed by salicylic acid (SA) as a proton donor with proton acceptors of different strength, on fluorescence spectra of SA in non-aqueous solutions have been investigated. Infrared spectra of studied systems have been analyzed in order to elucidate the ground state structure of the complexes formed. It has been found that at the room temperature in dilute solutions in non-polar or slightly polar aprotic solvents, where the SA molecule is not involved in intermolecular hydrogen bonding, the position of the main (blue) fluorescence component is determined by the excited state intramolecular proton transfer (ESIPT) in the lowest singlet excited state S 1. With increasing proton acceptor ability of the environment, when formation of weak or middle strength intermolecular H-bonds is possible, the emission band shifts gradually to lower frequency, the quantum yield falls and poorly resolved doublet structure becomes more pronounced, especially in the solvents containing heavy bromine atoms. As a possible reason for these effects, coupling between the S 1 and closely lying triplet term is considered. With the strongest proton acceptors like aliphatic amines, intermolecular proton transfer with ionic pair formation in the ground state and double (intra- and intermolecular) proton transfer in the excited state take place, resulting in a blue shift of the emission band. Similar emission is typical for the SA anion in aqueous solutions. The p Ka value of SA in S 1 state has been found to be 3.1. Such a small value can be explained taking into account the ESIPT reaction following the excitation. The SA complex with pyridine exhibits emission spectrum containing both molecular-like and anion-like bands with relative intensities strongly dependent on the temperature and solvent properties. The most probable origin of this dual emission is the molecular-ionic tautomerism caused by the existence of two potential minima and reversible intermolecular proton transfer in the excited state.

Denisov, G. S.; Golubev, N. S.; Schreiber, V. M.; Shajakhmedov, Sh. S.; Shurukhina, A. V.

1997-12-01

217

Theory of elastic interaction of colloidal particles in nematic liquid crystals near one wall and in the nematic cell  

NASA Astrophysics Data System (ADS)

We apply the method developed [Chernyshuk and Lev, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.041701 81, 041701 (2010)] for theoretical investigation of colloidal elastic interactions between axially symmetric particles in the confined nematic liquid crystal near one wall and in the nematic cell with thickness L. Both cases of homeotropic and planar director orientations are considered. Particularly, dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions of the one particle with the wall and within the nematic cell are found as well as corresponding two particle elastic interactions. A set of results has been predicted: The effective power of repulsion between two dipole particles at height h near the homeotropic wall is reduced gradually from inverse 3 to 5 with an increase of dimensionless distance r/h; near the planar wall, the effect of dipole-dipole isotropic attraction is predicted for large distances r>rdd=4.76h; maps of attraction and repulsion zones are crucially changed for all interactions near the planar wall and in the planar cell; and one dipole particle in the homeotropic nematic cell was found to be shifted by the distance ?eq from the center of the cell. The proposed theory fits very well with experimental data for the confinement effect of elastic interaction between spheres in the homeotropic cell [Vilfan , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.101.237801 101, 237801 (2008)] in the range 1-1000 kT. The influence of the K24 and K13 terms as well as connection with other theoretical approaches are discussed.

Chernyshuk, S. B.; Lev, B. I.

2011-07-01

218

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

219

Structural analysis of bis-bispidine tetraazamacrocycle: Long-range weak interactions in a channeled organic crystal  

NASA Astrophysics Data System (ADS)

A new organic crystal containing one-dimensional channels has been obtained through the synthesis and self-assembly of tetraethoxy bis-bispidine tetraazamacrocycles. The pre-fabricated macrocyclic cavities stack on each other to form ordered channels with highly basic inner cores. Based on the data of the single crystal structure, analysis of a 3D matrix indicates that weak directional interactions such as long-range Csbnd H⋯O hydrogen bonds and Nsbnd C⋯Osbnd C dipole-dipole interactions play an important role in the molecular alignment.

Wang, Zhuo; Islam, Md. Jahirul; Vukotic, V. Nicholas

2015-02-01

220

(1)H-(13)C Hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins.  

PubMed

(13)C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure (1)H-(13)C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the (1)H-(13)C hetero-nuclear dipolar interactions of (13)C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of (13)C(3) labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples. PMID:19896874

Wu, Chin H; Das, Bibhuti B; Opella, Stanley J

2010-02-01

221

1H- 13C hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins  

NASA Astrophysics Data System (ADS)

13C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure 1H- 13C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the 1H- 13C hetero-nuclear dipolar interactions of 13C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of 13C 3 labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples.

Wu, Chin H.; Das, Bibhuti B.; Opella, Stanley J.

2010-02-01

222

An assay for intermolecular exchange of alpha crystallin  

NASA Technical Reports Server (NTRS)

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

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

1992-01-01

223

The excited-states intermolecular potential energy surfaces of the Ar-CS2 van der Waals complex: Ab initio study  

NASA Astrophysics Data System (ADS)

The sixteen lowest potential energy surfaces (PESs) of the electronically excited Ar-CS2 van der Waals (vdW) complex are calculated in the singlet state. PESs are obtained based on the vertical excitation of the complex containing the linear geometry ground electronic state (1?g+) of CS2 molecule to the valence excited electronic states. The computational method involves EOM-CCSD with the aug-cc-pVDZ basis set augmented with a set of midbond functions (3s3p2d1f1g). It was found that some forbidden electronic transitions like 1?g+?1?g in the CS2 monomer become possible due to the presence of the Ar atom. The interaction PESs with the visible well-depth for all of the configurations are globally fitted to an analytic function in order to estimate the isotropic dipole-dipole (C60) and dipole-quadrupole (C80) coefficients of the excited states of the complex.

Farrokhpour, H.; Tozihi, M.

2014-08-01

224

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

225

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

226

Intermolecular iodine-iodine interactions in bis(pyridine-3-carboxylato)[tetrakis(4-iodophenyl)porphyrinato]tin(IV) and bis(pyrimidine-5-carboxylato)[tetrakis(4-iodophenyl)porphyrinato]tin(IV).  

PubMed

Crystals of bis(pyridine-3-carboxylato)[tetrakis(4-iodophenyl)porphyrinato]tin(IV) dimethylformamide sesquisolvate, [Sn(C44H24I4N4)(C6H4NO2)2]·1.5C3H7NO, (I), and bis(pyrimidine-5-carboxylato)[tetrakis(4-iodophenyl)porphyrinato]tin(IV) dimethylformamide sesquisolvate, [Sn(C44H24I4N4)(C5H3N2O2)2]·1.5C3H7NO, (II), exhibit interporphyrin iodine-iodine halogen bonds, which direct the supramolecular assembly of the porphyrin entities into halogen-bonded layers. Each molecule interacts with its four nearest neighbours within the layer via eight I···I interactions at approximately 3.8 and 4.0?Å. The two structures are isomorphous and isometric, with the metalloporphyrin complexes located on centres of crystallographic inversion. PMID:24005511

Titi, Hatem M; Patra, Ranjan; Goldberg, Israel

2013-09-01

227

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

PubMed

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

Tsuzuki, Seiji; Hayamizu, Kikuko; Seki, Shiro

2010-12-16

228

4,5-Diamino­benzene-1,2-dicarbonitrile  

PubMed Central

The mol­ecular skeleton of the title mol­ecule, C8H6N4, is essentially planar [maximum deviation from the mean plane of 0.037?(2)?Å]. All N atoms are involved in the formation of inter­molecular N—H?N hydrogen bonds. The crystal packing exhibits also dipole–dipole inter­actions between the cyano groups of neighbouring mol­ecules [C?C 3.473?(2)?Å]. PMID:21582556

Zhang, Xiuwen; Wang, Wei; Jiang, Jianzhuang; Ni, Zhonghai

2009-01-01

229

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

Microsoft Academic Search

[Zn(bispicam)2]2+ as a hydrogen-bond donor and three free halides (Cl?, Br? and I?) as hydrogen-bond acceptors were employed to investigate the role of non-classical C\\/N–H?X hydrogen bonding for construction of polymeric compounds. Three zinc salts (ZnCl2, ZnBr2 and ZnI2) were reacted with bis(2-pyridylmethyl)amine (bispicam) to produce [Zn(bispicam)2]Cl21, [Zn(bispicam)2]Br22 and [Zn(bispicam)2]I23. Hydrogen bonding interactions between Namine–H and C–H of [Zn(bispicam)2]2+ cations

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

2008-01-01

230

Quantum Hall effects in fast-rotating Fermi gases with anisotropic dipolar interaction  

SciTech Connect

We investigate fast rotating quasi-two-dimensional dipolar Fermi gases in the quantum Hall regime. By tuning the direction of the dipole moments with respect to the z axis, the dipole-dipole interaction becomes anisotropic in the x-y plane. For a soft confining potential we find that, as we tilt the angle of the dipole moments, the system evolves from a {nu}=1/3 Laughlin state with dipoles being polarized along the z axis to a series of ground states characterized by distinct mean total angular momentum, and finally to an anisotropic integer quantum Hall state. During the transition from the fractional regime to the integer regime, we find that the density profile of the system exhibits crystal-like structures. We map out the ground states as a function of the tilt angle and the confining potential, revealing the competition of the isotropic confining potential and both the isotropic and anisotropic components of the dipole-dipole interaction.

Qiu, R.-Z.; Yi, S. [Key Laboratory of Frontiers in Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190 (China); Kou, Su-Peng [Department of Physics, Beijing Normal University, Beijing 100875 (China); Hu, Z.-X. [Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Wan Xin [Zhejiang Institute of Modern Physics, Zhejiang University, Hangzhou 310027 (China)

2011-06-15

231

On the temperature dependence of the frequency of intermolecular vibrations in liquids  

SciTech Connect

A new approach to the treatment of low-frequency vibrational spectra of liquids, which is being developed by the authors on the basis of concepts of variation of the effective radius of interaction during intermolecular vibrations, is used for interpretation of data on the temperature dependence of the position of these spectra. Using two polar organic liquids, chloroform and chlorobenzene, as an example, calculated values of spectral shifts of intermolecular-vibration bands in the temperature range from 300 to 483 K are shown to be in reasonably good agreement with experiments. The authors feel that the approach under investigation holds promise for deriving direct information on the analytic form of the total interaction potential in a liquid from low-frequency vibrational spectra. 11 refs., 2 tabs.

Bakhshiev, N.G.; Libov, V.S. [Vavilov State Optical Institute, St. Petersburg (Russian Federation)

1994-11-01

232

Improved thermal stability of Langmuir-Blodgett films through an intermolecular hydrogen bond and metal complex  

NASA Astrophysics Data System (ADS)

Langmuir-Blodgett (LB) films of N-octadecanoyl-L-alanine and its silver and zinc complexes have been investigated by variable-temperature Fourier transform infrared transmission spectroscopy. The thermal stability of LB films is improved through an intermolecular hydrogen bond and metal complex. The intermolecular hydrogen-bonding interaction between hydrophilic head groups in the same monolayers and the metal complex between one head group and another in the neighboring monolayers considerably increase the interaction between the corresponding hydrophobic alkyl chains. It is shown that the transformation of the triclinic subcell packing of the molecules in the LB films prior to and after the silver complex into hexagonal packing occurs before the phase transition accompanied with a change in molecular orientation. The phase transition behavior of the LB films is varied from a small temperature interval to large one depending on the hydrogen bond and metal complex.

Du, Xuezhong; Liang, Yingqiu

2004-01-01

233

Multidimensional intermolecular dynamics from tunable far-infrared laser spectroscopy: Angular-radial coupling in the intermolecular potential  

E-print Network

Multidimensional intermolecular dynamics from tunable far-infrared laser spectroscopy: Angular] havebeenaccessedby tunable far-infrared laserspectroscopy.The measuredvibrational band origins of transitions the application of tunable far-infrared (TFIR) laser spec- troscopy to the measurementof the intermolecular vibra

Cohen, Ronald C.

234

Limits on possible new spin-spin interactions between neutrons from measurements of the Longitudinal Spin Relaxation Rate of Polarized $^{3}$He Gas  

E-print Network

New particles with masses in the sub-eV range have been predicted by various theories beyond the Standard Model. Some can induce new spin-spin interactions between fermions. Existing constraints on such interactions between nucleons with mesoscopic ranges (millimeters to nanometers) are quite poor. Polarized $^{3}$He gas is an especially clean system to use to constrain these possible new spin-spin interactions because the spin-independent atomic potential between helium atoms is well-characterized experimentally. The small effects from binary atomic collisions in a polarized gas from magnetic dipole-dipole and other possible weak spin-spin interactions which lead to spin relaxation can be calculated perturbatively. We compare existing measurements of the longitudinal spin relaxation rate $\\Gamma_{1}$ of polarized $^3$He gas with theoretical calculations and set a $1\\sigma$ upper bound on the pseudoscalar coupling strength $g_p$ for possible new neutron-neutron dipole-dipole interactions of $g_p^{(n)}g_p^{(n)...

Fu, Changbo

2011-01-01

235

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

236

Superfluidity and solid order in a two-component Bose gas with dipolar interactions in an optical lattice  

NASA Astrophysics Data System (ADS)

In this paper, we study an extended bosonic t-J model in an optical lattice, which describes two-component hard-core bosons with nearest-neighbor pseudospin interactions and, also, inter- and intraspecies dipole-dipole interactions. In particular, we focus on the case in which two-component hard-core bosons have antiparallel polarized dipoles with each other. The global phase diagram is studied by means of the Gutzwiller variational method and also quantum Monte Carlo (QMC) simulations. Both calculations show that a striped solid order, besides a checkerboard one, appears as a result of the dipole-dipole interactions. By QMC, we find that two kinds of supersolids (SSs) form, i.e., checkerboard SS and striped SS, and we also verify the existence of an exotic phase between the striped solid and the checkerboard SS. Finally, by QMC, we study the t-J-like model, which was recently realized experimentally by A. de Paz et al. [Phys. Rev. Lett. 111, 185305 (2013), 10.1103/PhysRevLett.111.185305].

Kuno, Yoshihito; Suzuki, Keita; Ichinose, Ikuo

2014-12-01

237

Quantitative tomographic imaging of intermolecular FRET in small animals  

PubMed Central

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

2012-01-01

238

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

2012-12-01

239

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

PubMed

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

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

2015-02-14

240

Mechanism of Intermolecular Electron Transfer in Bionanostructures  

NASA Astrophysics Data System (ADS)

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

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

241

Many-body dipole interactions  

NASA Astrophysics Data System (ADS)

This dissertation presents the study of controllable but strong long-range interaction between dipoles. In particular, we investigate the excitation and interaction between atoms in a cold gas where the collisional time is much greater than the interaction time between neighboring Rydberg atoms. In addition to quantum systems, we also examine the excitation properties of a collection of classical electric dipoles created by optically driving metallic nanospheres. We use various theoretical techniques to simulate these systems, including the direct numerical solutions to Schrodinger's equation, a Monte Carlo method, and a simple coupled point-dipole model. We first perform simulations involving the excitation of a collection of cold atoms to Rydberg states. When the interaction energy between excited atoms is large enough to shift multiply-excited states out of resonance with the tightly tuned excitation laser, the number of atoms able to be excited is suppressed, creating a dipole blockade effect. The blockade effect offers exciting possibilities in the control of quantum bits, which is crucial for the development of quantum computing. We also examined the effects of density variation with respect to the the dipole blockade with three different models. We then simulate the coherent interactions between Rydberg atoms. If the atoms are excited into states where the dipole-dipole interaction between them allows for resonant energy transfer to occur, then one state can freely hop from one atom to the next via the dipole-dipole interaction. We generated band structures for one, two, and three dimensional lattices and characterized the nature of the coherent hopping. This hopping is also studied in both a perfect and non-perfect lattice case which should be possible to examine experimentally. Next, we simulate the effect of special excitation pulses on a cold gas of atoms. First a rotary echo sequence is used to examine the coherent nature of a frozen Rydberg gas. If collective excitation and de-excitation is present with little or no source of dephasing, after these pulses the system should be returned to a state with few excitations, and a strong echo signal should occur. We investigate systems that should display a perfect echo and systems where the interaction between atoms reduces the echo signal. A spin echo sequence is also used on a system of coherent hopping excitations, and we simulate how the strength of a spin echo signal is affected by thermal motion. Finally, we describe the dipole-dipole interactions between a linear array of optically driven metallic nanospheres. These classical model calculations incorporate the full electric field generated by an oscillating electric dipole. The effects due to retardation of the generated electric field must be taken into account and several interesting effects are explored such as the ability to preferentially excite specific nanospheres.

Hernandez, Jesus V.

242

Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.  

PubMed

Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as ??(w)(0) = 1206 ± 2 J/mol and ?H(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations. PMID:24328234

Velaga, Srinath C; Anderson, Brian J

2014-01-16

243

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

SciTech Connect

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

Salam, A., E-mail: salama@wfu.edu [Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109 (United States)

2013-12-28

244

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

NASA Astrophysics Data System (ADS)

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

Salam, A.

2013-12-01

245

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

NASA Astrophysics Data System (ADS)

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

Pereira, André M.; Pereira, Clara; Silva, Ana S.; Schmool, David S.; Freire, Cristina; Grenèche, Jean-Marc; Araújo, João P.

2011-06-01

246

Proinsulin intermolecular interactions during secretory trafficking in pancreatic ? cells.  

PubMed

Classically, exit from the endoplasmic reticulum (ER) is rate-limiting for secretory protein trafficking because protein folding/assembly occurs there. In this study, we have exploited "hPro-CpepSfGFP," a human proinsulin bearing "superfolder" green fluorescent C-peptide expressed in pancreatic ? cells where it is processed to human insulin and CpepSfGFP. Remarkably, steady-state accumulation of hPro-CpepSfGFP and endogenous proinsulin is in the Golgi region, as if final stages of protein folding/assembly were occurring there. The Golgi regional distribution of proinsulin is dynamic, influenced by fasting/refeeding, and increased with ? cell zinc deficiency. However, coexpression of ER-entrapped mutant proinsulin-C(A7)Y shifts the steady-state distribution of wild-type proinsulin to the ER. Endogenous proinsulin coprecipitates with hPro-CpepSfGFP and even more so with hProC(A7)Y-CpepSfGFP. Using Cerulean and Venus-tagged proinsulins, we find that both WT-WT and WT-mutant proinsulin pairs exhibit FRET. The data demonstrate that wild-type proinsulin dimerizes within the ER but accumulates at a poorly recognized slow step within the Golgi region, reflecting either slow kinetics of proinsulin hexamerization, steps in formation of nascent secretory granules, or other unknown molecular events. However, in the presence of ongoing misfolding of a subpopulation of proinsulin in ? cells, the rate-limiting step in transport of the remaining proinsulin shifts to the ER. PMID:23223446

Haataja, Leena; Snapp, Erik; Wright, Jordan; Liu, Ming; Hardy, Alexandre B; Wheeler, Michael B; Markwardt, Michele L; Rizzo, Mark; Arvan, Peter

2013-01-18

247

Pigment spectra and intermolecular interaction potentials in glasses and proteins.  

PubMed

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 beta-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 (S(2) band of beta-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. PMID:17557783

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

2007-10-01

248

Supporting information for "Accurate intermolecular interactions at dramatically  

E-print Network

+SAPT with empirical dispersion" Ka Un Lao and John M. Herbert Optimized values of the range separation parameter@chemistry.ohio-state.edu S1 #12;Table S1: Optimized range separation parameters () for monomers. Monomer /bohr-1 Ionization.3393 HCN 0.35 13.9377 indole 0.10 7.8064 ammonia 0.10 10.6694 phenol 0.10 8.5962 pyrazine 0.20 10.4075 2

Herbert, John

249

Intermolecular vibrational spectra of C3v CXY3 Molecular Liquids, CHCl3, CHBr3, CFBr3, and CBrCl3.  

PubMed

We report the quality anisotropic intermolecular vibrational spectra within the frequency range 0.5-800 cm(-1) of four C(3v) CXY(3) molecular liquids, CHCl(3), CHBr(3), CFBr(3), and CBrCl(3), by means of femtosecond optical-heterodyne-detected Raman-induced Kerr effect spectroscopy. The results show that the first moment of the intermolecular vibrational spectrum is proportional to the square root of the value of the surface tension divided by the liquid density. This implies that the intermolecular vibrational spectrum reflects the bulk properties of the liquids. To understand the molecular-level aspects of the intermolecular vibrational spectra of the liquids, the spectra are compared with the molecular properties such as molecular weight, rotational constants, and bimolecular interaction energy. Overall, the first moment of the spectrum moderately correlates to the inverse square roots of both the molecular weight and the fast rotational constant. Therefore, the molecular properties are responsible for the intermolecular vibrational spectrum. Plots of the first moment of the intermolecular vibrational spectrum vs the square root of the value of the simple bimolecular interaction energy divided by the molecular surface area and the molecular weight show a linear correlation in the case of the oblate symmetric top molecular liquids, CHCl(3), CHBr(3), and CFBr(3). However, CBrCl(3), which is a prolate symmetric top molecular liquid, does not show the same correlation for the oblate molecular liquids. PMID:21749053

Shirota, Hideaki; Kato, Tatsuya

2011-08-18

250

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

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

251

Controlling the interactions of a few cold Rb Rydberg atoms by radiofrequency-assisted Förster resonances  

E-print Network

Long-range interactions between cold Rydberg atoms, which are used in many important applications, can be enhanced using F\\"orster resonances between collective many-body states controlled by an external electric field. Here we report on the first experimental observation of highly-resolved radio-frequency-assisted F\\"orster resonances in a few cold Rb Rydberg atoms. We also observed radio-frequency-induced F\\"orster resonances which cannot be tuned by a dc electric field. They imply an efficient transition from van der Waals to resonant dipole-dipole interaction due to Floquet sidebands of Rydberg levels appearing in the rf-field. This method can be applied to enhance the interactions of almost arbitrary Rydberg atoms with large principal quantum numbers.

D. B. Tretyakov; V. M. Entin; E. A. Yakshina; I. I. Beterov; C. Andreeva; I. I. Ryabtsev

2014-12-04

252

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

NASA Astrophysics Data System (ADS)

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

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

2000-05-01

253

Finite Ion-Size Effects Dominate the Interaction between Charged Colloidal Particles at an Oil-Water Interface  

NASA Astrophysics Data System (ADS)

The electrostatic interaction of charged spherical colloids trapped at an interface between a nonpolar medium and water is analyzed. Complementary experiments provide consistent values for the dipole-dipole interaction potential over a wide range of interparticle distances. After accounting for the contribution from the compact inner double layer arising from the finite size of the counterions, we demonstrate quantitative agreement between experiments and nonlinear Poisson-Boltzmann theory. We find that the inner layer contribution dominates the electrostatic interaction in the far field for particles pinned at the interface. This result is fundamentally different from screened electrostatic interactions in the bulk and could contribute to the further understanding of the structure of the compact counterion layer in highly charged systems.

Masschaele, Kasper; Park, Bum Jun; Furst, Eric M.; Fransaer, Jan; Vermant, Jan

2010-07-01

254

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

NASA Astrophysics Data System (ADS)

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

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

2010-08-01

255

Intermolecular potential for binding of protonated peptide ions with perfluorinated hydrocarbon surfaces.  

PubMed

An analytic potential energy function was developed to model both short-range and long-range interactions between protonated peptide ions and perfluorinated hydrocarbon chains. The potential function is defined as a sum of two-body potentials of the Buckingham form. The parameters of the two-body potentials were obtained by fits to intermolecular potential energy curves (IPECs) calculated for CF4, which represents the F and C atoms of a perfluoroalkane chain, interacting with small molecules chosen as representatives of the main functional groups and atoms present in protonated peptide ions: specifically, CH4, NH3, NH4(+), and HCOOH. The IPECs were calculated at the MP2/aug-cc-pVTZ level of theory, with basis set superposition error (BSSE) corrections. Good fits were obtained for an energy range extending up to about 400 kcal/mol. It is shown that the pair potentials derived from the NH3/CF4 and HCOOH/CF4 fits reproduce acceptably well the intermolecular interactions in HCONH2/CF4, which indicates that the parameters obtained for the amine and carbonyl atoms may be transferable to the corresponding atoms of the amide group. The derived potential energy function may be used in chemical dynamics simulations of collisions of peptide-H(+) ions with perfluorinated hydrocarbon surfaces. PMID:24779856

Pratihar, Subha; Kohale, Swapnil C; Vázquez, Saulo A; Hase, William L

2014-05-22

256

Enhanced superradiance effect in a system of interacting two-level atoms and crossover from coherent to many-atom multiphoton relaxation regime  

NASA Astrophysics Data System (ADS)

We study effects of direct interatomic interaction on cooperative processes in atom-photon dynamics. Using a model of two-level atoms with Ising-type interaction as an example, it is demonstrated that interparticle interaction can promote cooperative radiative relaxation. For small number of atoms this results in inhibition of incoherent spontaneous decay leading to the regime of collective pulse relaxation. Above superradiance threshold increase in delay time and enhancement of superradiance is occurred. In the case of strong interaction (as compared to excitation energy of an atom) transition to the regime of multiphoton relaxation occurs, which we discuss using a simple model of two atoms in a high-Q single mode cavity. It is shown that such transition is accompanied by Rabi oscillations involving many-atom multiphoton states. Dephasing effect of dipole-dipole interaction and solitonic mechanism of relaxation are discussed as well.

Lukyanets, S.; Bevzenko, D.

2011-11-01

257

Controlling the self-assembly of magnetic nanoparticles by competing dipolar and isotropic particle interactions.  

PubMed

Control over the self-assembly of magnetic nanoparticles (MNP) into superstructures due to different types of coupling is of interest in the development of "bottom-up" fabrication schemes. Here we realize a simple strategy for the systematic variation of particle interaction potential in magnetic nanoparticles. This is achieved by varying the effective surface potential by means of a co-surfactant introduced in the course of the synthesis process. As a consequence, the ability to form chain-like assemblies is affected by the resulting balance of attractive and repulsive forces. We use electron microscopy, electron diffraction, and light scattering methods to study a series of cobalt nanoparticles as a characteristic example of ferromagnetic MNP. We demonstrate experimentally and substantiate theoretically that the observed behavior results from a balance between magnetic dipole-dipole, steric, and electrostatic interactions. PMID:25265589

Hod, Manuela; Dobbrow, Celin; Vaidyanathan, Mukanth; Guin, Debanjan; Belkoura, Lhoussaine; Strey, Reinhard; Gottlieb, Moshe; Schmidt, Annette M

2014-12-15

258

Strong impact of protonation and deprotonation on intermolecular Coulombic decay  

NASA Astrophysics Data System (ADS)

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

Kryzhevoi, Nikolai V.; Cederbaum, Lorenz S.

2012-11-01

259

A model intermolecular potential for hydrogen fluoride including polarizability  

NASA Astrophysics Data System (ADS)

An intermolecular potential model for hydrogen fluoride is proposed. This has a central Lennard-Jones part, three axial charges fixed by the dipole and quadrupole moments, and anisotropic polarizability. Good agreement with experimental values is found for the dimer, liquid and crystal lattice structures and energies, and for the second virial coefficient.

Murad, S.; Mansour, K. A.; Powles, J. G.

1986-10-01

260

Photochemistry of intermolecular C-H bond activation reactions  

SciTech Connect

Goals at the onset were to obtain photophysical and photochemical data on transition-metal organometallic complexes which undergo light-induced intermolecular C-H bond activation reactions with hydrocarbon substrates. The complexes included these of rhodium and rhenium with such as cyclopentadiene, CO, phosphine, pyridines, etc.

Lees, A.J.

1994-09-01

261

Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.  

PubMed

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of ?-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment. PMID:22634414

Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

2012-09-01

262

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

PubMed Central

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

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

2014-01-01

263

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.

264

Intermolecular Forces and the Glass Transition  

E-print Network

Random first order transition theory is used to determine the role of attractive and repulsive interactions in the dynamics of supercooled liquids. Self-consistent phonon theory, an approximate mean field treatment consistent with random first order transition theory, is used to treat individual glassy configurations, while the liquid phase is treated using common liquid state approximations. The transition temperature $T^{*}_{A} $, the temperature where the onset of activated behavior is predicted by mean field theory, the lower crossover temperature $T_{c}^{*}$ where barrierless motions actually occur through fractal or stringy motions, and $T^{*}_{K} $, the Kauzmann temperature, are calculated in addition to $T^{*}_{g} $, the glass transition temperature that corresponds to laboratory cooling rates. Both the isobaric and isochoric behavior in the supercooled regime are studied, providing results for $\\Delta C_{V} $ and $\\Delta C_{p} $ that can be used to calculate the fragility as a function of density and pressure, respectively. The predicted variations in the $\\alpha$-relaxation time with temperature and density conform to the empirical density-temperature scaling relations found by Casalini and Roland. We thereby demonstrate the microscopic origin of their observations. Finally, the relationship first suggested by Sastry between the spinodal temperature and the Kauzmann temperatures, as a function of density, is examined. The present microscopic calculations support the existence of an intersection of these two temperatures at sufficiently low temperatures.

Randall W. Hall; Peter G. Wolynes

2007-09-13

265

Direct detection of intermolecular forces by atomic force microscopy  

NASA Astrophysics Data System (ADS)

The phenomenon of adhesion appears in various applications of everyday life, ranging from PostIt Notes(TM) and Scotch Tape(TM), to the assembly of aircraft and space shuttles. However, adhesion on the molecular scale is fundamentally different from the adhesion that we experience in the macroscopic world. While macroscopic objects require special adhesives or glues to bind them together, microscale and nanoscale objects and molecules commonly have a high affinity to adhere to each other. A detailed description of intermolecular forces is therefore of key importance in order to understand a wide range of phenomena, ranging from macroscopic properties of materials to molecular recognition. Two key aspects of the atomic force microscope (AFM), namely its sensitivity to sub-nanoNewton forces and its very sharp probe, offer the opportunity to measure interactions between very small numbers of molecules. Through chemical tailoring of both substrates and AFM probes with self-assembled monolayers (SAMs), measurements of forces acting between specific functional groups can be measured. Furthermore, the force required to rupture a single chemical bond can be obtained by a detailed analysis of the histograms of rupture forces. A new model was derived to examine the relationship between the various experimental variables and the shape of histograms of rupture forces when discrete chemical bonds are formed between the AFM probe and substrate. Calculations based on the model demonstrated that in measurements aimed at detecting single bond rupture forces, strict limits are put on the size of the AFM probe, the relative magnitude of the interfacial energies and the bond formation probability. These results were used in two experimental systems where the single bond rupture force was successfully measured: (i) the abstraction of a single Au-S complex from an Au coated AFM probe; and (ii) the rupture of a single charge-transfer (CT) complex between tetramethylphenylenediamine (TMPD) and tetracyanoquinodimethane (TCNQ). Measurements involving only one molecule at a time were conducted using polymer chains chemically grafted to the AFM probe and substrate. In these measurements, the effect of the solvent on the elasticity of the poly-ethylene-propylene oligomers was directly observed in the force-elongation profile.

Skulason, Hjalti

266

Intermolecular forces and scaling relations between heterogeneous macromolecular surfaces  

NASA Astrophysics Data System (ADS)

Most theories regarding the behavior of intermolecular forces assume perfectly smooth surfaces with well-defined chemical and material properties. In this thesis, three separate systems are studied to explore the accuracy of this assumption in very different situations. In the first system, the effects of milli-molar amounts of dissolved gas (the amount typically present in normal atmospheric conditions) have been studied at a pristine oil/water interface. It was found that the removal of the dissolved gas significantly increased the lifetime of the oil droplets, effectively reducing the long-range hydrophobic attractive force present under standard conditions. In the second system, the effect of varying normal and lateral roughness of solid surfaces in understanding the long-range steric forces and shorter-range adhesive (van der Waals) forces are studied. Various techniques to reproducibly control and vary the roughness were developed for a number of different types of polymeric surfaces. A strong correlation between the roughness and the repulsive steric force was observed for randomly rough surfaces. Similar scaling relations between the roughness and the magnitude of the adhesive force were measured. Friction measurements between these surfaces show that even a few nanometers of roughness significantly reduces the critical shear stress required to initiate sliding. However, the coefficient of friction was relatively unaffected by the range of roughness considered, in agreement with the macroscopic Amontons' law. The third and final system dealt with the properties of adsorbed layers of polyampholytes (containing both positively and negatively charged groups), as opposed to the more common classes of neutral polymers or polyelectrolytes. These measurements took advantage of a naturally occurring family of proteins (a class of polyampholytes), known as tau, which exist in six different well-defined lengths and charge densities. Force measurements were made with a Surface Forces Apparatus (SFA) in various ionic solution conditions, combined with high resolution imaging by an Atomic Force Microscope (AFM). Scaling relations between the magnitude and range of the total interaction force are shown depending on the total length as well as the relative ratio of positive to negative groups along the backbone of the macromolecule.

Rosenberg, Kenneth J.

267

Intermolecular disulfide bond formation promotes immunoglobulin aggregation: Investigation by fluorescence correlation spectroscopy.  

PubMed

Protein aggregation generally results from association between hydrophobic regions of individual monomers. However, additional mechanisms arising from specific interactions, such as intermolecular disulfide bond formation, may also contribute to the process. The latter is proposed to be the initiating pathway for aggregation of immunoglobulin (IgG), which is essential for triggering its immune response. To test the veracity of this hypothesis, we have employed fluorescence correlation spectroscopy to measure the kinetics of aggregation of IgG in separate experiments either allowing or inhibiting disulfide formation. Fluorescence correlation spectroscopy measurements yielded a diffusion time (?D ) of ?200 µsec for Rhodamine-labeled IgG, corresponding to a hydrodynamic radius (RH ) of 56 Å for the IgG monomer. The aggregation kinetics of the protein was followed by monitoring the time evolution of ?D under conditions in which its cysteine residues were either free or blocked. In both cases, the progress curves confirmed that aggregation proceeded via the nucleation-dependent polymerization pathway. However, for aggregation in the presence of free cysteines, the lag times were shorter, and the aggregate sizes bigger, than their respective counterparts for aggregation in the presence of blocked cysteines. This result clearly demonstrates that formation of intermolecular disulfide bonds represents a preferred pathway in the aggregation process of IgG. Fluorescence spectroscopy showed that aggregates formed in experiments where disulfide formation was prevented denatured at lower concentration of guanidine hydrochloride than those obtained in experiments where the disulfides were free to form, indicating that intermolecular disulfide bridging is a valid pathway for IgG aggregation. Proteins 2015; 83:169-177. © 2014 Wiley Periodicals, Inc. PMID:25371040

Nag, Moupriya; Bera, Kallol; Basak, Soumen

2015-01-01

268

Intermolecular Potential Energy Surfaces from Far Infrared Laser Spectroscopy of Weakly Bound Complexes  

Microsoft Academic Search

High resolution far infrared laser spectroscopy of the low frequency intermolecular vibrations in weakly bound complexes provides the means to probe intermolecular forces with unprecedented detail and accuracy. This thesis describes two important new directions of research. The role of many-body effects in intermolecular forces, a largely unexplored subject, has been investigated through far infrared spectroscopy of the Ar_2HCl van

Matthew John Elrod

1994-01-01

269

ChemTeacher Resource: Flash Interactive Digital Overheads  

NSDL National Science Digital Library

Allows the user to interactively and visually learn chemistry. Subtopics include Microscpic World, Atomic Structure, Molecular Structure, Intermolecular Forces, Chemical Reactions, Chemical Kinetics, Chemical Equilibrium

2012-08-01

270

Transition-density-fragment interaction approach for exciton-coupled circular dichroism spectra  

NASA Astrophysics Data System (ADS)

A transition-density-fragment interaction (TDFI) method for exciton-coupled circular dichroism (ECCD) spectra is proposed. The TDFI method was previously developed for excitation-energy transfer, which led to the successful estimation of the electronic coupling energy between donor and accepter molecules in xanthorhodopsin [K. J. Fujimoto and S. Hayashi, J. Am. Chem. Soc. 131, 14152 (2009)]. In the present study, the TDFI scheme is extended to the ECCD spectral calculation based on the matrix method and is applied to a dimerized retinal (all-trans N-retinylidene-L-alanine Schiff base) chromophore. Compared with the dipole-dipole and transition charge from ESP methods, TDFI has a much improved description of the electronic coupling. In addition, the matrix method combined with TDFI can reduce the computational costs compared with the full quantum-mechanical calculation. These advantages of the present method make it possible to accurately evaluate the CD Cotton effects observed in experiment.

Fujimoto, Kazuhiro J.

2010-09-01

271

Transition-density-fragment interaction approach for exciton-coupled circular dichroism spectra.  

PubMed

A transition-density-fragment interaction (TDFI) method for exciton-coupled circular dichroism (ECCD) spectra is proposed. The TDFI method was previously developed for excitation-energy transfer, which led to the successful estimation of the electronic coupling energy between donor and accepter molecules in xanthorhodopsin [K. J. Fujimoto and S. Hayashi, J. Am. Chem. Soc. 131, 14152 (2009)]. In the present study, the TDFI scheme is extended to the ECCD spectral calculation based on the matrix method and is applied to a dimerized retinal (all-trans N-retinylidene-L-alanine Schiff base) chromophore. Compared with the dipole-dipole and transition charge from ESP methods, TDFI has a much improved description of the electronic coupling. In addition, the matrix method combined with TDFI can reduce the computational costs compared with the full quantum-mechanical calculation. These advantages of the present method make it possible to accurately evaluate the CD Cotton effects observed in experiment. PMID:20886918

Fujimoto, Kazuhiro J

2010-09-28

272

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

NASA Astrophysics Data System (ADS)

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

Lebedev, A. V.

2015-01-01

273

Absorption Spectra of Quantum Aggregates Interacting via Long-Range Forces  

SciTech Connect

We present a simple formula by which the shape of the absorption spectrum of an aggregate of quantum 'monomers' (cold atoms, molecules, quantum dots, nanoparticles, etc.) interacting via dipole-dipole forces can be calculated from the averaged spectrum of the quantum monomer itself. Spectral broadening, due to a wide variety of causes, is included explicitly so that the formula is applicable not only to the idealization of a discrete spectrum but also to the practical situation of a continuously broadened spectrum. In simple cases, analytic results are obtained showing the strong dependence of the aggregate spectrum on the precise nature of the broadening of the quantum monomer spectrum. The formula is compared with results of exact diagonalization of model aggregate Hamiltonians and with experiment.

Eisfeld, A.; Briggs, J.S. [Theoretische Quantendynamik, Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany)

2006-03-24

274

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

275

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

PubMed

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

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

2014-08-01

276

Intra- and intermolecular hydrogen bonding in acetylacetone and benzoylacetone derived enaminone derivatives  

NASA Astrophysics Data System (ADS)

The structure and hydrogen bonding in solution of acetylacetone and benzoylacetone derived enaminone derivatives, 1a-1d and 2a-2d, have been studied by a combination of experimental (NMR and UV spectroscopies) and theoretical (PM6 and DFT) methods. It has been shown that all studied compounds predominantly existed in the localised keto-amine tautomeric form in solution as found also in the solid state. Significant line-broadening and down-field chemical shifts of NH and OH protons have strongly indicated that both groups formed hydrogen bonds, which has further been supported by quantum chemical calculations. Temperature and concentration dependent NMR measurements have pointed towards the fact that NH protons are engaged in strong intramolecular hydrogen bonds of the NH⋯Odbnd C type in both solvents. On the other hand, OH protons are involved in weaker intermolecular hydrogen bonding with solvent molecules in DMSO, while in chloroform intermolecular interactions between two molecules dominate. The results presented in this paper can be used for better understanding and further exploiting properties these ligands possess, especially their bioactivity.

Lazi?, Vedrana; Jurkovi?, Mihaela; Jedna?ak, Tomislav; Hrenar, Tomica; Vukovi?, Jelena Parlov; Novak, Predrag

2015-01-01

277

Intermolecular ?-Strand Networks Avoid Hub Residues and Favor Low Interconnectedness: A Potential Protection Mechanism against Chain Dissociation upon Mutation  

PubMed Central

Altogether few protein oligomers undergo a conformational transition to a state that impairs their function and leads to diseases. But when it happens, the consequences are not harmless and the so-called conformational diseases pose serious public health problems. Notorious examples are the Alzheimer's disease and some cancers associated with a conformational change of the amyloid precursor protein (APP) and of the p53 tumor suppressor, respectively. The transition is linked with the propensity of ?-strands to aggregate into amyloid fibers. Nevertheless, a huge number of protein oligomers associate chains via ?-strand interactions (intermolecular ?-strand interface) without ever evolving into fibers. We analyzed the layout of 1048 intermolecular ?-strand interfaces looking for features that could provide the ?-strands resistance to conformational transitions. The interfaces were reconstructed as networks with the residues as the nodes and the interactions between residues as the links. The networks followed an exponential decay degree distribution, implying an absence of hubs and nodes with few links. Such layout provides robustness to changes. Few links per nodes do not restrict the choices of amino acids capable of making an interface and maintain high sequence plasticity. Few links reduce the “bonding” cost of making an interface. Finally, few links moderate the vulnerability to amino acid mutation because it entails limited communication between the nodes. This confines the effects of a mutation to few residues instead of propagating them to many residues via hubs. We propose that intermolecular ?-strand interfaces are organized in networks that tolerate amino acid mutation to avoid chain dissociation, the first step towards fiber formation. This is tested by looking at the intermolecular ?-strand network of the p53 tetramer. PMID:24733378

Feverati, Giovanni; Achoch, Mounia; Vuillon, Laurent; Lesieur, Claire

2014-01-01

278

Role of dipolar interaction in magnetic hyperthermia  

NASA Astrophysics Data System (ADS)

The dynamic properties of magnetic nanoparticles are known to be substantially influenced by the dipole-dipole interaction. In this paper we study how this affects the efficiency of magnetic hyperthermia experiments. In particular we ask whether it is possible to use the dipolar interaction as a mechanism to increase the heat released by the nanoparticles, thus improving the application. The investigation is carried out via numerical simulations based on a mean-field model developed to include the dipolar interaction in the Fokker-Planck equation describing the time evolution of the system. Both the linear and nonlinear regimes (related to the amplitude of the external magnetic field) are studied in detail. It is shown that even moderate changes in the particle concentration may have substantial effects on the magnetization dynamics of the system, being capable of increasing or decreasing the heat released by orders of magnitude, depending on the values of other system parameters. It is found that the dipolar interaction can be used to increase the dissipation of magnetically soft particles, but should be avoided in the case of hard particles.

Landi, Gabriel T.

2014-01-01

279

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

SciTech Connect

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

Sadat, M E [University of Cincinnati; Patel, Ronak [University of Cincinnati; Sookoor, Jason [University of Cincinnati; Bud'ko, Sergey L [Ames Laboratory; Ewing, Rodney C [Stanford University; Zhang, Jiaming [Stanford University; Xu, Hong [Shanghai Jiao Tong University; Wang, Yilong [Tongji University School of Medicine; Pauletti, Giovanni M [University of Cincinnati; Mast, David B [University of Cincinnati; Shi, Donglu [University of Cincinnati

2014-09-01

280

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

281

Intramolecular and intermolecular vibrational energy relaxation of CH 2I 2 dissolved in supercritical fluid  

NASA Astrophysics Data System (ADS)

A pump-probe experiment was performed to examine vibrational population relaxation of diiodomethane (CH 2I 2) molecule dissolved in supercritical CO 2. Using an apparatus with femtosecond time resolution, we observed the contributions of intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) separately. IVR and VET rates were measured with varying solvent densities at a constant temperature. It is shown that the IVR rate is not density dependent while the VET rate increases with increasing density from 0.4 to 0.8 g cm-3. This observation suggests that the rate of the VET process is determined by solute-solvent collisions whereas the IVR rate is not much affected by solute-solvent interaction.

Sekiguchi, K.; Shimojima, A.; Kajimoto, O.

2002-04-01

282

The kinetic peculiarities of intermolecular proton transfer from NH groups of octa( m-trifluoromethylphenyl)tetraazaporphin in the nitrogen base-benzene system  

NASA Astrophysics Data System (ADS)

The acid-base interaction of octa( m-trifluoromethylphenyl)tetraazaporphin with nitrogen bases in benzene was studied. The rates of intermolecular transfer of sterically screened NH group protons from octa( m-trifluoromethylphenyl)tetraazaporphin to n-butylamine and tert-butylamine were found to be low. A scheme of the process was suggested. The influence of the nature of bases on the kinetic parameters of acid-base interactions was studied.

Petrov, O. A.; Khelevina, O. G.; Kuzmina, E. L.

2010-09-01

283

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. PMID:19927125

Lee, Seungjoo; Antony, Lizamma; Hartmann, Rune; Knaus, Karen J; Surewicz, Krystyna; Surewicz, Witold K; Yee, Vivien C

2010-01-01

284

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

NASA Astrophysics Data System (ADS)

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

Minami, Takuya; Nakano, Masayoshi

2015-01-01

285

Theoretical calculation of self-broadening coefficients for the ?5 band of methyl chloride at various temperatures  

NASA Astrophysics Data System (ADS)

Self-broadening coefficients of transitions belonging to the ?5 band of methyl chloride have been calculated using a semi-classical model based on the Anderson-Tsao-Curnutte (ATC) theory, including some improvements proposed by Robert and Bonamy. The calculations show the predominance of the dipole-dipole interaction. To better match the experimental measurements performed at room temperature in our previous work, a cut-off of the intermolecular distance has been used. The rotational J and K dependencies of the calculated self-broadening coefficients have been clearly observed and are consistent with our previous measurements.

Barbouchi Ramchani, A.; Jacquemart, D.; Dhib, M.; Aroui, H.

2014-02-01

286

Transetherification on Polyols by Intra- and Intermolecular Nucleophilic Substitutions  

PubMed Central

Transetherification on polyols involving intra- and intermolecular nucleophilic substitutions is reported. Di- or trialkoxide formation of propane-1,3-diol or 2-(hydroxymethyl)propane-1,3-diol derivatives by NaH triggers the reaction via oxetanes formation, where the order to add NaH and a polyol significantly influences the yields of products. It was demonstrated that the protective group on the pentaerythritol skeleton is apparently transferred to the hydrophilic and hydrophobic chain molecules bearing a leaving group in one-step, and a protective group conversion from tosyl to benzyl was successful using a benzyl-appending triol to afford a desired product in 67% yield. PMID:24663293

Muraoka, Takahiro; Adachi, Kota; Chowdhury, Rainy; Kinbara, Kazushi

2014-01-01

287

Intermolecular vibrations and fast relaxations in supercooled ionic liquids.  

PubMed

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. PMID:21721643

Ribeiro, Mauro C C

2011-06-28

288

Intra-and Intermolecular Effects on 1 H Chemical Shifts in a Silk Model Peptide  

E-print Network

Intra- and Intermolecular Effects on 1 H Chemical Shifts in a Silk Model Peptide Determined by High peptide (Ala-Gly)15 for the crystalline domain of Bombyx mori silk fibroin in silk I and silk II structures, including a treatment of both intra- and intermolecular arrangements. Silk I and silk II

Williamson, Mike P.

289

Van der Waals interactions: Evaluations by use of a statistical mechanical method  

NASA Astrophysics Data System (ADS)

In this work the induced van der Waals interaction between a pair of neutral atoms or molecules is considered by use of a statistical mechanical method. With use of the Schrödinger equation this interaction can be obtained by standard quantum mechanical perturbation theory to second order. However, the latter is restricted to electrostatic interactions between dipole moments. So with radiating dipole-dipole interaction where retardation effects are important for large separations of the particles, other methods are needed, and the resulting induced interaction is the Casimir-Polder interaction usually obtained by field theory. It can also be evaluated, however, by a statistical mechanical method that utilizes the path integral representation. We here show explicitly by use of this method the equivalence of the Casimir-Polder interaction and the van der Waals interaction based upon the Schrödinger equation. The equivalence is to leading order for short separations where retardation effects can be neglected. In recent works [J. S. Høye, Physica A 389, 1380 (2010), 10.1016/j.physa.2009.12.003; Phys. Rev. E 81, 061114 (2010)], 10.1103/PhysRevE.81.061114, the Casimir-Polder or Casimir energy was added as a correction to calculations of systems like the electron clouds of molecules. The equivalence to van der Waals interactions indicates that the added Casimir energy will improve the accuracy of calculated molecular energies. Thus, we give numerical estimates of this energy including analysis and estimates for the uniform electron gas.

Høye, Johan S.

2011-10-01

290

Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding  

PubMed Central

Background The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation. Results A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interaction energy by about 20–40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place. Conclusion The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N) in conventional pairwise Van der Waals interactions. PMID:17880673

Finkelstein, Alexei V

2007-01-01

291

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

NASA Astrophysics Data System (ADS)

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

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

2006-08-01

292

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

293

Resonant Auger decay driving intermolecular Coulombic decay in molecular dimers  

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

294

Resonant Auger decay driving intermolecular Coulombic decay in molecular dimers.  

PubMed

In 1997, it was predicted that an electronically excited atom or molecule placed in a loosely bound chemical system (such as a hydrogen-bonded or van-der-Waals-bonded cluster) could efficiently decay by transferring its excess energy to a neighbouring species that would then emit a low-energy electron. This intermolecular Coulombic decay (ICD) process has since been shown to be a common phenomenon, raising questions about its role in DNA damage induced by ionizing radiation, in which low-energy electrons are known to play an important part. It was recently suggested that ICD can be triggered efficiently and site-selectively by resonantly core-exciting a target atom, which then transforms through Auger decay into an ionic species with sufficiently high excitation energy to permit ICD to occur. Here we show experimentally that resonant Auger decay can indeed trigger ICD in dimers of both molecular nitrogen and carbon monoxide. By using ion and electron momentum spectroscopy to measure simultaneously the charged species created in the resonant-Auger-driven ICD cascade, we find that ICD occurs in less time than the 20?femtoseconds it would take for individual molecules to undergo dissociation. Our experimental confirmation of this process and its efficiency may trigger renewed efforts to develop resonant X-ray excitation schemes for more localized and targeted cancer radiation therapy. PMID:24362568

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

2014-01-30

295

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

296

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

297

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

298

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

299

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

2012-05-01

300

ParAB-mediated intermolecular association of plasmid P1 parS sites.  

PubMed

The P1 plasmid partition system depends on ParA-ParB proteins acting on centromere-like parS sites for a faithful plasmid segregation during the Escherichia coli cell cycle. In vivo we placed parS into host E. coli chromosome and on a Sop(+) F plasmid and found that the stability of a P1 plasmid deleted for parA-parB could be partially restored when parB was expressed in trans. In vitro, parS, conjugated to magnetic beads could capture free parS DNA fragment in presence of ParB. In vitro, ParA stimulated ParB-mediated association of intermolecular parS sites in an ATP-dependent manner. However, in the presence of ADP, ParA reduced ParB-mediated pairing to levels below that seen by ParB alone. ParB of P1 pairs the parS sites of plasmids in vivo and fragments in vitro. Our findings support a model whereby ParB complexes P1 plasmids, ParA-ATP stimulates this interaction and ParA-ADP inhibits ParB pairing activity in a parS-independent manner. PMID:22018490

Kaur, Tranum; Al Abdallah, Qusai; Nafissi, Nafiseh; Wettig, Shawn; Funnell, Barbara E; Slavcev, Roderick A

2011-12-20

301

Bimodal Intermolecular Proton Transfer in Acid-Base Neutralization Reactions in Water  

NASA Astrophysics Data System (ADS)

We present an ultrafast mid-infrared study of excited-state intermolecular proton transfer in photoacid-base pairs in water. Observation of bimodal reaction dynamics demand refinement of the established Eigen-Weller mechanism.

Mohammed, O. F.; Rini, M.; Dreyer, J.; Magnes, B.-Z.; Pines, D.; Nibbering, E. T. J.; Pines, E.

302

Intermolecular cyclocondensation reaction of 3,4-dihydropyrimidine-2-thione under the Mitsunobu reaction conditions  

Microsoft Academic Search

A self-intermolecular cyclocondensation reaction of 3,4-dihydropyrimidine-2-thione (DHPM) to give a novel tricyclic structure containing DHPM core in the presence of diethyl azodicarboxylate (DEAD) and triphenylphosphine (TPP) at room temperature is reported.

Yu Xia Da; Zhang Zhang; Zheng Jun Quan

2011-01-01

303

Determining the Intermolecular Potential Energy in a Gas: A Physical Chemistry Experiment  

ERIC Educational Resources Information Center

Describes an experiment in which gas viscosity coefficients over a large temperature range are used to determine the parameters of the intermolecular potential energy and other properties such as virial coefficients. (MLH)

Olbregts, J.; Walgraeve, J. P.

1976-01-01

304

Intermolecular and intramolecular FRET between two spectrally overlapping green fluorescent protein variants fused to two  

E-print Network

573 Intermolecular and intramolecular FRET between two spectrally overlapping green fluorescent fluorescent proteins within a living cell and follow the time course of the changes in FRET corresponding cyan fluorescent protein FLIM fluorescence lifetime imaging microscopy FRET fluorescence resonance

305

Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes  

E-print Network

Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes inter- acting dipole (TID) polarization model has been developed for liquid alkanes and amides provides an adequate description of structural and thermodynamic prop- erties for liquid alkanes

Minnesota, University of

306

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

307

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

308

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

NASA Astrophysics Data System (ADS)

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

Mackelprang, C. E.

1980-09-01

309

The effect of the intermolecular potential formulation on the state-selected energy exchange rate coefficients in N2-N2 collisions.  

PubMed

The rate coefficients for N2-N2 collision-induced vibrational energy exchange (important for the enhancement of several modern innovative technologies) have been computed over a wide range of temperature. Potential energy surfaces based on different formulations of the intramolecular and intermolecular components of the interaction have been used to compute quasiclassically and semiclassically some vibrational to vibrational energy transfer rate coefficients. Related outcomes have been rationalized in terms of state-to-state probabilities and cross sections for quasi-resonant transitions and deexcitations from the first excited vibrational level (for which experimental information are available). On this ground, it has been possible to spot critical differences on the vibrational energy exchange mechanisms supported by the different surfaces (mainly by their intermolecular components) in the low collision energy regime, though still effective for temperatures as high as 10,000 K. It was found, in particular, that the most recently proposed intermolecular potential becomes the most effective in promoting vibrational energy exchange near threshold temperatures and has a behavior opposite to the previously proposed one when varying the coupling of vibration with the other degrees of freedom. PMID:24590423

Kurnosov, Alexander; Cacciatore, Mario; Laganà, Antonio; Pirani, Fernando; Bartolomei, Massimiliano; Garcia, Ernesto

2014-04-01

310

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

NASA Astrophysics Data System (ADS)

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

Ghoufi, Aziz; Malfreyt, Patrice

2006-12-01

311

Intermolecular Casimir-Polder forces in water and near surfaces  

NASA Astrophysics Data System (ADS)

The Casimir-Polder force is an important long-range interaction involved in adsorption and desorption of molecules in fluids. We explore Casimir-Polder interactions between methane molecules in water, and between a molecule in water near SiO2 and hexane surfaces. Inclusion of the finite molecular size in the expression for the Casimir-Polder energy leads to estimates of the dispersion contribution to the binding energies between molecules and between one molecule and a planar surface.

Thiyam, Priyadarshini; Persson, Clas; Sernelius, Bo E.; Parsons, Drew F.; Malthe-Sørenssen, Anders; Boström, Mathias

2014-09-01

312

Gold(I)-Catalyzed Intra-and Intermolecular Hydroamination of Unactivated Junliang Zhang, Cai-Guang Yang, and Chuan He*  

E-print Network

-based molecules, such as amines, anilines, carboxyamides, carbamates, alkylsulfona- mides, or sulfamates that carbamates also work as nucleophiles in intramolecular additions. Table 1. Intermolecular Hydroamination

He, Chuan

313

Electrostatic model for treating long-range lateral interactions between polar molecules adsorbed on metal surfaces  

NASA Astrophysics Data System (ADS)

A classical polarizable point-dipole model for the adsorption of polar molecules on metal surfaces is presented. The main usefulness of the model is that lattice sums are represented by simple functions in closed form. This allows a simple extrapolation of adsorption energies of polar molecules—as calculated by first-principles calculations employing periodic boundary conditions—to the zero-coverage limit. Such an extrapolation is rather important for the proper evaluation of adsorption energy of highly polar molecules, because their long-range lateral interactions can extend beyond the nearest-neighbor distances of 50 bohrs. Moreover, the dependence of the adsorption energy on the orientation and configuration of molecular dipoles can be straightforwardly analyzed. It is demonstrated that an accumulation of polar molecules on the surface is favored provided that the molecular dipoles point parallel to the surface in the adsorbed state, whereas adsorbed molecules displaying dipoles oriented perpendicular to the surface would prefer to stay well separated due to repulsive lateral interactions. Further, the model is used to analyze the density-functional theory (DFT) calculated data of two polar molecules, triazole and benzotriazole, adsorbed onto Cu(111) surface. The DFT-calculated adsorption energies are about -0.5 eV, and it is shown that the main contribution to the molecule-surface bonding comes from the dipole-dipole electrostatic interactions.

Kokalj, Anton

2011-07-01

314

Study of organic compounds-water interactions by partition in aqueous two-phase systems.  

PubMed

Partition coefficients of fourteen organic compounds were determined in 10 or 20 different polymer/polymer aqueous two-phase systems (ATPS) all at physiological pH (0.15M NaCl in 0.01M phosphate buffer, pH 7.4). Solute-specific coefficients characterizing different types of solute-water interactions for the compounds examined were determined by the multiple linear regression analysis. It is shown that (i) the partition behavior for the polar organic compounds is affected not only by dipole-dipole and hydrogen-bond interactions with aqueous environment but, notably, in most cases also by dipole-ion interactions; (ii) it is possible to predict partition behavior for compounds with pre-determined solute-specific coefficients in ATPS with characterized solvent features; and (iii) linear combinations of the solute-specific coefficients for the organic compounds might be useful in the development of quantitative structure-activity relationship (QSAR) analysis to describe their odor detection threshold. PMID:24268821

Madeira, Pedro P; Bessa, Ana; Teixeira, Miguel A; Álvares-Ribeiro, Luís; Aires-Barros, M Raquel; Rodrigues, Alírio E; Zaslavsky, Boris Y

2013-12-27

315

Chemical origin of blue- and redshifted hydrogen bonds: Intramolecular hyperconjugation and its coupling with intermolecular hyperconjugation  

NASA Astrophysics Data System (ADS)

Upon formation of a H bond Y ⋯H-XZ, intramolecular hyperconjugation n(Z )??*(X-H) of the proton donor plays a key role in red- and blueshift characters of H bonds and must be introduced in the concepts of hyperconjugation and rehybridization. Intermolecular hyperconjugation transfers electron density from Y to ?*(X-H) and causes elongation and stretch frequency redshift of the X-H bond; intramolecular hyperconjugation couples with intermolecular hyperconjugation and can adjust electron density in ?*(X-H); rehybridization causes contraction and stretch frequency blueshift of the X-H bond on complexation. The three factors—intra- and intermolecular hyperconjugations and rehybridization determine commonly red- or blueshift of the formed H bond. A proton donor that has strong intramolecular hyperconjugation often forms blueshifted H bonds.

Li, An Yong

2007-04-01

316

Intermolecular potential functions from spectroscopic properties of weakly bound complexes. Third progress report, July 1, 1991--June 30, 1992  

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.

1992-08-01

317

Explosives sensing by using electron-rich supramolecular polymers: role of intermolecular hydrogen bonding in significant enhancement of sensitivity.  

PubMed

We demonstrate here that supramolecular interactions enhance the sensitivity towards detection of electron-deficient nitro-aromatic compounds (NACs) over discrete analogues. NACs are the most commonly used explosive ingredients and are common constituents of many unexploded landmines used during World War II. In this study, we have synthesised a series of pyrene-based polycarboxylic acids along with their corresponding discrete esters. Due to the electron richness and the fluorescent behaviour of the pyrene moiety, all the compounds act as sensors for electron-deficient NACs through a fluorescence quenching mechanism. A Stern-Volmer quenching constant determination revealed that the carboxylic acids are more sensitive than the corresponding esters towards NACs in solution. The high sensitivity of the acids was attributed to supramolecular polymer formation through hydrogen bonding in the case of the acids, and the enhancement mechanism is based on an exciton energy migration upon excitation along the hydrogen-bond backbone. The presence of intermolecular hydrogen bonding in the acids in solution was established by solvent-dependent fluorescence studies and dynamic light scattering (DLS) experiments. In addition, the importance of intermolecular hydrogen bonds in solid-state sensing was further explored by scanning tunnelling microscopy (STM) experiments at the liquid-solid interface, in which structures of self-assembled monolayer of the acids and the corresponding esters were compared. The sensitivity tests revealed that these supramolecular sensors can even detect picric acid and trinitrotoluene in solution at levels as low as parts per trillion (ppt), which is much below the recommended permissible level of these constituents in drinking water. PMID:25187022

Gole, Bappaditya; Song, Wentao; Lackinger, Markus; Mukherjee, Partha Sarathi

2014-10-13

318

The Ar-HF intermolecular potential: Overtone spectroscopy and ab initio calculations  

NASA Astrophysics Data System (ADS)

The vibrational dependence of the intermolecular potential of Ar-HF is investigated through the spectra of levels correlating with HF(v=3). We have previously reported measurements of the (vbKn)=(3000), (3100), and (3110) levels of Ar-HF using intracavity laser-induced fluorescence in a slit supersonic jet [J. Chem. Phys. 98, 2497 (1993)]. These levels are found to be well reproduced (within 0.1 cm-1) by the Ar-HF H6(4,3,2) potential [J. Chem. Phys. 96, 6752 (1992)]. The second overtone experiments are extended to include the (3002) state which is coupled to (3110) through Coriolis interaction, and the (3210) state which is more sensitive to higher-order anisotropic terms in the potential. The observations establish that the level (3002) lies 0.229 cm-1 below (3110), with upper state rotational constant B=0.085 89 cm-1. This is in good accord with the predictions of the H6(4,3,2) potential. The (3210) state lies at 11 484.745 cm-1 with B=0.099 79 cm-1. The band origin is 1.7 cm-1 higher than predicted, and thus contains important new information on the vibrational dependence of the potential. Several detailed features of the spectra can be explained using the H6(4,3,2) potential. The Q-branch lines of the (3210)?(0000) band show evidence of a weak perturbation, which can be explained in terms of mixing with the (3112) state. The (3210) spectrum exhibits parity-dependent rotational predissociation and the widths of the P- and R-branch lines and the magnitude of the l-type doubling can be explained in terms of coupling to the (3200) state, which is estimated to lie 4 cm-1 below the (3210) state. The Q-branch lines show a predissociation cutoff above Q(16); this is in reasonable agreement with the predictions of the H6(4,3,2) potential, but suggests that the binding energy calculated for the potential may be about 1 cm-1 too large. To examine the potential further, high-level ab initio calculations are performed, with an efficient basis set incorporating bond functions. The calculations give a well depth of 92%-95% of that of the H6(4,3,2) potential at ?=0° for v=0 and v=3, respectively; this is in line with earlier results on rare gas pairs. The calculations also reproduce the anisotropy of the H6(4,3,2) potential and its vibrational dependence. The dependence of the intermolecular potential on HF bond length is found explicitly.

Chang, Huan-C.; Tao, Fu-Ming; Klemperer, William; Healey, Catherine; Hutson, Jeremy M.

1993-12-01

319

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

320

Intermolecular potential energy surface and thermophysical properties of ethylene oxide.  

PubMed

A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C2H4O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide. PMID:25362314

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

2014-10-28

321

Intermolecular potential energy surface and thermophysical properties of ethylene oxide  

NASA Astrophysics Data System (ADS)

A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C2H4O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

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

2014-10-01

322

Weak intermolecular H-bonds as a tool to design 2D self-organized molecular architectures: Tailoring a “Scottish Tartan” open network  

NASA Astrophysics Data System (ADS)

We show here that weak intermolecular H-bonds ( E = 2-3 kcal/mol) can be used as an efficient tool to design supramolecular self-organized 2D periodic networks. These weak attractive and directional forces can take place when the molecules bear weakly acidic hydrogen atoms (such as aromatic CH) and electron-attracting groups (such as NO 2). We demonstrate the versatility of using weak H-bonds to tailor 2D networks with a simple model molecule, an adequately substituted benzene derivative bearing a nitro group, two aliphatic chains, but deprived of strongly acidic H atom (such as OH, NH, etc.). We show by means of scanning tunnelling microscopy (STM) that this compound self-assembles on Au(1 1 1) into a 2D open network through multiple intermolecular weak H-bonds between aromatic H-atoms and the O-atoms of the NO 2 groups. The prominent role of weak H-bonds in the 2D arrangement of this molecule on gold is supported by ab initio calculations of intermolecular interaction energies ( E = 3.1 kcal/mol) and H-bond lengths ( L = 2.55 Å). Based on both experimental and theoretical results, we propose a 2D model where molecules first interlock to each other into quartets through eight weak H-bonds and then into quartets-of-quartets through interchain Van der Waals interactions, the final packing being reminiscent of a Scottish Tartan. It is worth noting that such an arrangement leaves a square-shape central cavity (1.1 × 1.1 nm 2) in the unit cell thus providing opportunities towards guest-host systems of a new type.

Popoff, Alexandre; Fichou, Denis

2009-11-01

323

Intermolecular CH\\ctdot O hydrogen bonds in formyl-substituted diphenylhexatriene, a [2 + 2] photoreactive organic solid: Crystal structure and IR, NMR spectroscopic evidence  

NASA Astrophysics Data System (ADS)

( E, E, E)-1,6-di(4-formylphenyl)-1,3,5-hexatriene ( 1) undergoes [2 + 2] photocycloaddition in the solid state, while the unsubstituted parent, ( E, E, E)-1,6-diphenyl-1,3,5-hexatriene (DPH), is photochemically inert as we reported previously. Although the steering effect of the formyl group for the photoreaction is very clear, the crystal structure of 1 had been unknown. In this study, single crystals of 1 suitable for X-ray diffraction (XRD) analysis were prepared and the crystal structure was investigated. The molecules in crystal are linked through intermolecular CH⋯O-type hydrogen bonds involving formyl groups to form a 3D structure of ?-stacked crystal packing arrangement with intermolecular distance of 3.926 Å (= b), less than the Schmidt's criteria of 4.2 Å for the [2 + 2] photoreaction. The existence of CH⋯O hydrogen bonds is evidenced by FT-IR, 1H and 13C NMR spectroscopic measurements. For the IR peak assignments, ab initio and DFT calculations were performed. The solid-state 1H and 13C NMR spectra were measured using the CRAMPS and CP/MAS techniques, respectively. Owing to the small CH⋯O angular dependence of the interaction energy (directionality), the CH⋯O hydrogen bonds are formed in a multiple manner. Thus, although being rather weak, these hydrogen bonds play a decisive role in constructing the [2 + 2] photoreactive crystal structure, without any other stronger intermolecular interactions coexisting.

Sonoda, Yoriko; Goto, Midori; Ikeda, Takuji; Shimoi, Yukihiro; Hayashi, Shigenobu; Yamawaki, Hiroshi; Kanesato, Masatoshi

2011-12-01

324

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

2013-11-21

325

Investigations of the intermolecular forces between RDX and polyethylene by force-distance spectroscopy and molecular dynamics simulations.  

PubMed

The development of novel nanoenergetic materials with enhanced bulk properties requires an understanding of the intermolecular interactions occurring between molecular components. We investigate the surface interactions between 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) and polyethylene (PE) crystals on the basis of combined use of molecular dynamics (MD) simulations and force-distance spectroscopy, in conjunction with Lifshitz macroscopic theory of van der Waals forces between continuous materials. The binding energy in the RDX-PE system depends both on the degree of PE crystallinity and on the RDX crystal face. Our MD simulations yield binding energies of approximately 132 and 120 mJ/m(2) for 100% amorphous and 100% crystalline PE on RDX (210), respectively. The average value is about 36% greater than our experimental value of 81 ± 15 mJ/m(2) for PE (?48% amorphous) on RDX (210). By comparison, Liftshitz theory predicts a value of about 79 mJ/m(2) for PE interacting with RDX. Our MD simulations also predict larger binding energies for both amorphous and crystalline PE on RDX (210) compared to the RDX (001) surface. Analysis of the interaction potential indicates that about 60% of the binding energy in the PE-RDX system is due to attractive interactions between HPE-ORDX and CPE-NRDX pairs of atoms. Further, amorphous PE shows a much longer interaction distance than crystalline PE with the (210) and (001) RDX surfaces due to the possibility of larger polymer elongations in the case of amorphous PE as strain is applied. Also, we report estimates of the binding energies of energetic materials RDX and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) with PE, propylene, polystyrene, and several fluorine-containing polymers using Lifshitz theory and compare these with reported MD calculations. PMID:24922563

Taylor, D E; Strawhecker, K E; Shanholtz, E R; Sorescu, D C; Sausa, R C

2014-07-10

326

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

SciTech Connect

By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

Chen, Yu-Chun; Tang, Ping-Han [Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan (China)] [Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan (China); Wu, Ten-Ming, E-mail: tmw@faculty.nctu.edu.tw [Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan (China) [Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan (China); National Center for Theoretical Sciences, Hsinchu 300, Taiwan (China)

2013-11-28

327

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

PubMed

By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given. PMID:24289362

Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

2013-11-28

328

Practical, Modular, and General Synthesis of 3-Coumaranones through Gold-Catalyzed Intermolecular Alkyne Oxidation Strategy.  

PubMed

A gold-catalyzed intermolecular alkyne oxidation for the preparation of 3-coumaranones has been developed. Using 8-isopropylquinoline N-oxides as oxidants, the reactions of o-ethynylanisoles afford versatile 3-coumaranones in moderate to good isolated yields. The synthetic utility of this chemistry is also indicated by the synthesis of the natural product sulfuretin. PMID:25287758

Shu, Chao; Liu, Rongfu; Liu, Shuang; Li, Jian-Qiao; Yu, Yong-Fei; He, Qiao; Lu, Xin; Ye, Long-Wu

2015-01-01

329

A homolytic oxy-functionalization mechanism: intermolecular hydrocarbyl migration from M-R to vanadate oxo.  

PubMed

A new mechanism for generating C-O bonds from metal-hydrocarbyls involving homolytic, intermolecular migration of the hydrocarbyl group to a vanadium oxo is reported. Responsible for the C-O bond in phenol formed by the reaction of OVCl3 with HgPh2, it may provide air-regenerable metal oxos a role in aerobic alkane oxidations. PMID:25096926

Cheng, Mu-Jeng; Nielsen, Robert J; Goddard, William A

2014-09-28

330

(Me3Si)3SiH-mediated intermolecular radical perfluoroalkylation reactions of olefins in water.  

PubMed

Perfluoroalkyl-substituted compounds are regarded as important components of fluorophors and for the introduction of fluorous tags into organic substrates. Their syntheses in organic solvents are achieved through different methods, among which, the addition of perfluoroalkyl radicals to unsaturated bonds represents a convenient choice. On the other hand, intermolecular radical reactions in water have attracted the attention of synthetic chemists as a strategic route to carbon-carbon bond formation reactions. In this paper we undertook the intermolecular addition of perfluoroalkyl radicals on electron rich alkenes and alkenes with electron withdrawing groups in water, mediated by silyl radicals, and obtained perfluoroalkyl-substituted compounds in fairly good yields. The radical triggering events employed consist of the thermal decomposition of an azo compound and the dioxygen initiation. Our results indicate that for intermolecular carbon-carbon bond formation reactions mediated by (Me(3)Si)(3)SiH, the decomposition of the azo compound 1,1'-azobis(cyclohexanecarbonitrile) (ACCN) is the best radical initiator. We also found that water exerts a relevant solvent effect on the rates of perfluoroalkyl radical additions onto double bonds and the H atom abstraction from the silane. Our account provides a versatile and convenient method to achieve perfluoroalkylation reactions of alkenes in water to render perfluoroalkylated alkanes as key intermediates in the synthesis of fluorophors and other fluorinated materials. This is the first report where perfluoroalkyl-substituted alkanes are synthesized through intermolecular radical carbon-carbon bond formation reactions in water, mediated by silyl radicals. PMID:20738111

Barata-Vallejo, Sebastián; Postigo, Al

2010-09-17

331

Intermolecular Dynamic Kinetic Resolution Cooperatively Catalyzed by an N-Heterocyclic Carbene and a Lewis Acid.  

PubMed

The ubiquitous structure of ?-lactones makes the development of new methods for their enantioselective and stereoselective synthesis an important ongoing challenge. The intermolecular dynamic kinetic resolution (DKR) of ?-halo-?-ketoesters cooperatively catalyzed by an N-heterocyclic carbene and a Lewis acid generates two contiguous stereocenters with remarkable diastereoselectivity through an oxidation/lactonization sequence. PMID:25447028

Wu, Zijun; Li, Fangyi; Wang, Jian

2014-11-28

332

Intermolecular vibration in the low-frequency Raman spectra of l-alanine crystal  

Microsoft Academic Search

The low-frequency, ? 150 cm-1, polarized Raman spectra of l-alanine single crystals determined by Wang and Storms can be interpreted simply in terms of the intermolecular vibrations, i.e., librations and\\/or translations, of the four oriented alanine molecules in the unit cell of the orthorhombic crystal.

Eugene Loh

1975-01-01

333

Using Molecular Dynamics Simulation to Reinforce Student Understanding of Intermolecular Forces  

ERIC Educational Resources Information Center

Intermolecular forces play an important role in many aspects of chemistry ranging from inorganic to biological chemistry. These forces dictate molecular conformation, species aggregation (including self-assembly), trends in solubility and boiling points, adsorption characteristics, viscosity, phase changes, surface tension, capillary action, vapor…

Burkholder, Phillip R.; Purser, Gordon H.; Cole, Renee S.

2008-01-01

334

Frontier orbital symmetry control of intermolecular electron transfer. Final report, September 15, 1988--December 31, 1994  

SciTech Connect

This report discusses the following topics: the recovery of intermolecular transfer parameters from fluorescence quenching in liquids; photoinduced intramolecular electron transfer in flexible donor/space/acceptor systems containing an extended unsaturated spacer; electron transfer sensitized reaction; the recovery of solute and fractal dimensions from electron transfer quenching data; and frontier orbital symmetry control of back electron transfer.

Stevens, B.

1997-07-01

335

Intermolecular vibrations and diffusive orientational dynamics of Cs condensed ring aromatic molecular liquids.  

PubMed

The ultrafast dynamics, including the intermolecular vibrations and the diffusive orientational dynamics, of the neat C(s) symmetry condensed ring aromatic molecular liquids benzofuran, 1-fluoronaphtalene, and quinoline were investigated for the first time by means of femtosecond Raman-induced Kerr effect spectroscopy. To understand the features of these C(s) condensed ring aromatic molecular liquids, reference singular aromatic molecular liquids, furan, fluorobenzene, pyridine, and benzene, were also studied. High quality low-frequency Kerr spectra of the aromatic molecular liquids were obtained by Fourier-transform deconvolution analysis of the measured Kerr transients. The Kerr spectra of the C(s) condensed ring aromatic molecular liquids are bimodal, as are those of the reference singular aromatic molecular liquids. The first moment of the intermolecular vibrational spectrum and the peak frequencies of the high- and low-frequency components in the broad spectrum band were compared with their molecular properties such as the rotational constants, molecular weight, and intermolecular (bimolecular) force. The comparisons show that the molecular volume (related to molecular weight and rotational constants) is a dominant property for the characteristic frequency of the entire intermolecular vibrational spectrum. The observed intramolecular vibrational modes in the Kerr spectra of the aromatic molecular liquids were also assigned on the basis of the ab initio quantum chemical calculation results. In their picosecond diffusive orientational dynamics, the slowest relaxation time constant for both the condensed ring and singular aromatic molecular liquids can be accounted for by the simple Stokes-Einstein-Debye hydrodynamic model. PMID:22060730

Shirota, Hideaki

2011-12-22

336

A New Intermolecular Potential Model for the n-Alkane Homologous Series  

E-print Network

A New Intermolecular Potential Model for the n- Alkane Homologous Series Jeffrey R. Errington model for the n-alkane homologous series has been developed, param- eterized to the vapor models. The simplest of hydrocarbons are the n-alkanes, which are flexible linear chains of methylene

337

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

E-print Network

and functionally similar. The boiling points of MeBr and MeI are 3.3 °C (37.9 °F) and 42.5 °C (108.5 °F) either in equal amounts or in various other mixing ratios. The boiling point of chloropicrin is 112 °C (233 °F). The application of liquid pesticides leads to soil wetting, mixing with water

Glaser, Rainer

338

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

PubMed

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

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

2014-10-14

339

Modeling and measurement of intermolecular interaction forces between cartilage ECM macromolecules  

E-print Network

The mechanical properties of cartilage tissue depend largely on the macromolecules that make up its extracellular matrix (ECM). Aggrecan is the most abundant proteoglycan in articular cartilage. It is composed of a core ...

Dean, Delphine Marguerite Denise, 1978-

2005-01-01

340

An approach to the origin of self-replicating system. I - Intermolecular interactions  

NASA Technical Reports Server (NTRS)

The present paper deals with the characteristics and potentialities of a recently developed computer-based molecular modeling system. Some characteristics of current coding systems are examined and are extrapolated to the apparent requirements of primitive prebiological coding systems.

Macelroy, R. D.; Coeckelenbergh, Y.; Rein, R.

1978-01-01

341

Self-assembly of pyrene derivatives on Au(111): substituent effects on intermolecular interactions.  

PubMed

The adsorption behaviour as well as the influence of bromine substituents on the formation of highly-ordered two-dimensional structures of pyrene derivatives on Au(111) are studied by a combination of scanning tunnelling microscopy (STM) and density functional theory (DFT) calculations. PMID:24905327

Pham, Tuan Anh; Song, Fei; Nguyen, Manh-Thuong; Stöhr, Meike

2014-11-25

342

Two-dimensional infrared spectroscopy of intermolecular hydrogen bonds in the condensed phase.  

PubMed

Hydrogen bonding plays a key role in the structural, physical, and chemical properties of liquids such as water and in macromolecular structures such as proteins. Vibrational spectroscopy is an important tool for understanding hydrogen bonding because it provides a way to observe local molecular geometries and their interaction with the environment. Linear vibrational spectroscopy has mapped characteristic changes of vibrational spectra and the occurrence of new bands that form upon hydrogen bonding. However, linear vibrational spectroscopy gives very limited insight into ultrafast dynamics of the underlying molecular interactions, such as the motions of hydrogen-bonded groups, energy dissipation and delocalization, and the fluctuations within hydrogen-bonded structures that occur in the ultrafast time domain. Nonlinear vibrational spectroscopy with its femtosecond time resolution can discern these dynamic processes in real time and has emerged as an important tool for unraveling molecular dynamics and for quantifying interactions that govern the vibrational and structural dynamics of hydrogen bonds. This Account reviews recent progress originating from third-order nonlinear methods of coherent multidimensional vibrational spectroscopy. Ultrafast dynamics of intermolecular hydrogen bonds are addressed for a number of prototype systems: hydrogen-bonded carboxylic acid dimers in an aprotic liquid environment, the disordered fluctuating hydrogen-bond network of liquid water, and DNA oligomers interacting with water. Cyclic carboxylic acid dimers display a rich scheme of vibrational couplings, resulting in OH stretching absorption bands with highly complex spectral envelopes. Two-dimensional spectroscopy of acetic acid dimers in a nonpolar liquid environment demonstrates that multiple Fermi resonances of the OH stretching mode with overtones and combination tones of fingerprint vibrations dominate both the 2D and linear absorption spectra. The coupling of the OH stretching mode with low-frequency hydrogen-bonding modes leads to additional progressions and coherent low-frequency hydrogen-bond motions in the subpicosecond time domain. In water, the 2D spectra reveal ultrafast spectral diffusion on a sub-100 fs time scale caused by the ultrafast structural fluctuations of the strongly coupled hydrogen-bond network. Librational motions play a key role for the ultrafast loss of structural memory. Spectral diffusion rates are enhanced by resonant transfer of OH stretching quanta between water molecules, typically occurring on a 100 fs time scale. In DNA oligomers, femtosecond nonlinear vibrational spectroscopy resolves NH and OH stretching bands in the highly congested infrared spectra of these molecules, which contain alternating adenine-thymine pairs. Studies at different levels of hydration reveal the spectral signatures of water molecules directly interacting with the phosphate groups of DNA and of a second water species forming a fluctuating environment around the DNA oligomers. We expect that the application of 2D infrared spectroscopy in an extended spectral range will reveal the intrinsic coupling between water and specific functional units of DNA. PMID:19425543

Elsaesser, Thomas

2009-09-15

343

Intermolecular potential parameters and combining rules determined from viscosity data  

SciTech Connect

The Law of Corresponding States has been demonstrated for a number of pure substances and binary mixtures, and provides evidence that the transport properties viscosity and diffusion can be determined from a molecular shape function, often taken to be a Lennard-Jones 12-6 potential, that requires two scaling parameters: a well depth {var_epsilon}{sub ij} and a collision diameter {sigma}{sub ij}, both of which depend on the interacting species i and j. We obtain estimates for {var_epsilon}{sub ij} and {sigma}{sub ij} of interacting species by finding the values that provide the best fit to viscosity data for binary mixtures, and compare these to calculated parameters using several 'combining rules' that have been suggested for determining parameter values for binary collisions from parameter values that describe collisions of like molecules. Different combining rules give different values for {sigma}{sub ij} and {var_epsilon}{sub ij} and for some mixtures the differences between these values and the best-fit parameter values are rather large. There is a curve in ({var_epsilon}{sub ij}, {sigma}{sub ij}) space such that parameter values on the curve generate a calculated viscosity in good agreement with measurements for a pure gas or a binary mixture. The various combining rules produce couples of parameters {var_epsilon}{sub ij}, {sigma}{sub ij} that lie close to the curve and therefore generate predicted mixture viscosities in satisfactory agreement with experiment. Although the combining rules were found to underpredict the viscosity in most of the cases, Kong's rule was found to work better than the others, but none of the combining rules consistently yields parameter values near the best-fit values, suggesting that improved rules could be developed.

Bastien, Lucas A.J.; Price, Phillip N.; Brown, Nancy J.

2010-05-07

344

Intermolecular potentials for simulations of collisions of SiNCS+ and (CH3)2SiNCS+ ions with fluorinated self-assembled monolayers  

NASA Astrophysics Data System (ADS)

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 DFT-D method (specifically, B97-D) was successfully tested against high-level wavefunction calculations performed on the smallest system investigated. The IPECs calculated at the B97-D level were fitted to analytical potentials of the Buckingham type. The calculations show that the parameters obtained from the fits involving CF4 are transferable to the miniSAM system, provided the fittings are conducted with caution, thus corroborating that CF4 is a good model for parameterizing intermolecular potentials for interactions of gases with F-SAM surfaces.

Nogueira, Juan José; Sánchez-Coronilla, Antonio; Marques, Jorge M. C.; Hase, William L.; Martínez-Núñez, Emilio; Vázquez, Saulo A.

2012-05-01

345

On the anisotropic intermolecular potential of biaxial apolar solutes in nematic solvents: Monte Carlo predictions and experimental data  

NASA Astrophysics Data System (ADS)

Recently, a new formulation has been proposed about a strictly short-range anisotropic potential acting on biaxial apolar particles dissolved in a uniaxial medium [Chem. Phys. Lett. 342, 375 (2001)], where the solute-solvent interactions are treated at a molecular level and the solute order parameters are calculated by making use of the Monte Carlo-Metropolis sampling scheme. In the present paper the cited model has been used for the study of 1,4-difluorobenzene, 1,4-dichlorobenzene, and 1,4-dibromobenzene molecules and the simulated order parameters have been compared with the 1H-NMR experimental data for the solutes in the nematic solvents ZLI1132 (a Merck commercial eutectic mixture of alkylcyclohexylcyanobenzenes and alkylcyclohexylcyanobiphenyl), EBBA [the N-(4-ethoxybenzylidene)-4'-n-butylaniline], and in the zero average electric field gradient nematic mixture 55 wt% ZLI1132+EBBA (the so-called "magic" mixture). The orientations predicted by the model match almost perfectly the experimental Saupe matrices of the molecules dissolved in the "magic" mixture: implications of this result are discussed in terms of nature of the interactions in the different nematic phases and reliability and effectiveness of the suggested intermolecular potential.

Celebre, Giorgio

2001-11-01

346

BRI2 homodimerizes with the involvement of intermolecular disulfide bonds  

PubMed Central

Familial British and Familial Danish Dementia (FBD and FDD) are two dominantly inherited neurodegenerative diseases that present striking similarities with Alzheimer’s disease. The genetic defects underlying those dementias are mutations in the gene that encodes for BRI2 protein. Cleavage of mutated BRI2 by furin releases the peptides ABri or ADan, which accumulate in the brains of patients. BRI2 normal function is yet unknown. To unwind aspects of its cellular role, we investigated the possibility that BRI2 forms dimers, based on structural elements of the protein, the GXXXG motif within its transmembrane domain and the odd number of cysteine residues. We found that BRI2 dimerizes in cells and that dimers are held via non-covalent interactions and via disulfide bridges between the cysteines at position 89. Additionally, we showed that BRI2 dimers are formed in the ER and appear at the cell surface. Finally, BRI2 dimers were found to exist in mouse brain. Revealing the physiological properties of BRI2 is critical in the elucidation of the deviations that lead to neurodegeneration. PMID:18440095

Tsachaki, Maria; Ghiso, Jorge; Rostagno, Agueda; Efthimiopoulos, Spiros

2009-01-01

347

Molecular nitrogen-N2 properties: The intermolecular potential and the equation of state  

NASA Astrophysics Data System (ADS)

Quantum mechanical (QM) high precision calculations were used to determine N2-N2 intermolecular interaction potential. Using QM numerical data the anisotropic potential energy surface was obtained for all orientations of the pair of the nitrogen molecules in the rotation invariant form. The new N2-N2 potential is in reasonably good agreement with the scaled potential obtained by van der Avoird et al. using the results of Hartree-Fock calculations [J. Chem. Phys. 84, 1629 (1986)]. The molecular dynamics (MD) of the N2 molecules has been used to determine nitrogen equation of state. The classical motion of N2 molecules was integrated in rigid rotor approximation, i.e., it accounted only translational and rotational degrees of freedom. Fincham [Mol. Simul. 11, 79 (1993)] algorithm was shown to be superior in terms of precision and energy stability to other algorithms, including Singer [Mol. Phys. 33, 1757 (1977)], fifth order predictor-corrector, or Runge-Kutta, and was therefore used in the MD modeling of the nitrogen pressure [S. Krukowski and P. Strak, J. Chem. Phys. 124, 134501 (2006)]. Nitrogen equation of state at pressures up to 30GPa (300kbars) and temperatures from the room temperature to 2000K was obtained using MD simulation results. Results of MD simulations are in very good agreement (the error below 1%) with the experimental data on nitrogen equation of state at pressures below 1GPa (10kbars) for temperatures below 1800K [R. T. Jacobsen et al., J. Phys. Chem. Ref. Data 15, 735 (1986)]. For higher temperatures, the deviation is slightly larger, about 2.5% which still is a very good agreement. The slightly larger difference may be attributed to the vibrational motion not accounted explicitly by rigid rotor approximation, which may be especially important at high temperatures. These results allow to obtain reliable equation of state of nitrogen for pressures up to 30GPa (300kbars), i.e., close to molecular nitrogen stability limit, determined by Nellis et al. [Phys. Rev. Lett. 53, 1661 (1984)].

Str?k, Pawe?; Krukowski, Stanis?aw

2007-05-01

348

Effect of external electric field on H-bonding and ?-stacking interactions in guanine aggregates.  

PubMed

The structure and electronic properties of guanine oligomers and ? stacks of guanine quartets (G-quartets) with circulene are investigated under an external field through first-principles calculations. An electric field induces nonplanarity in the guanine aggregates and also leads to an increase in the H-bond distances. The calculations reveal that the binding energy of the circulenes with G-quartets increases on application of an electric field along the stacking direction. The HOMO-LUMO gap decreases substantially under the influence of an external field. The contribution of a simple dipole-dipole interaction to the stability of the stacked system is also analyzed. The electric field along the perpendicular axis increases the dipole moments of the guanine dimer, trimer, and quartet. Such an increase in the dipole moment facilitates stacking with circulenes. The stability of G-quartet-circulene ? stacks depends on the phase of the dipole moment (in-phase or out-of-phase) induced by an external electric field. The stability of stacks of bowl-shaped circulenes with G-quartets depends on the direction of the applied field. PMID:23065813

Jissy, Akkarapattiakal K; Datta, Ayan

2012-12-21

349

Solubility and aggregation of Gly(5) in water.  

PubMed

Experimentally, the solubility of oligoglycines in water decreases as its length increases. Computationally, the free energy of solvation becomes more favorable with chain length for short (n = 1-5) oligoglycines. We present results of large scale simulations with over 600 pentaglycines at varying concentrations in explicit solvent to consider the mechanism of aggregation. The solubility limit of Gly5 for the force field used was calculated and compared with experimental values. We find that intermolecular interactions between pentaglycines are favored over interactions between glycine and water, leading to their aggregation. However, the interaction driving peptide associations, liquid-liquid phase separation, are not predominantly hydrogen bonding. Instead, non-hydrogen bonding interactions between partially charged atoms on the peptide backbone allow the formation of dipole-dipole and charge layering correlations that mechanistically stabilize the formation of large, stable peptide clusters. PMID:25019618

Karandur, Deepti; Wong, Ka-Yiu; Pettitt, B Montgomery

2014-08-14

350

Optical Activity Enhanced by Strong Inter-molecular Coupling in Planar Chiral Metamaterials  

PubMed Central

The polarization of light can be rotated in materials with an absence of molecular or structural mirror symmetry. While this rotating ability is normally rather weak in naturally occurring chiral materials, artificial chiral metamaterials have demonstrated extraordinary rotational ability by engineering intra-molecular couplings. However, while in general, chiral metamaterials can exhibit strong rotatory power at or around resonances, they convert linearly polarized waves into elliptically polarized ones. Here, we demonstrate that strong inter-molecular coupling through a small gap between adjacent chiral metamolecules can lead to a broadband enhanced rotating ability with pure rotation of linearly polarized electromagnetic waves. Strong inter-molecular coupling leads to nearly identical behaviour in magnitude, but engenders substantial difference in phase between transmitted left and right-handed waves. PMID:25209452

Kim, Teun-Teun; Oh, Sang Soon; Park, Hyun-Sung; Zhao, Rongkuo; Kim, Seong-Han; Choi, Wonjune; Min, Bumki; Hess, Ortwin

2014-01-01

351

Optical activity enhanced by strong inter-molecular coupling in planar chiral metamaterials.  

PubMed

The polarization of light can be rotated in materials with an absence of molecular or structural mirror symmetry. While this rotating ability is normally rather weak in naturally occurring chiral materials, artificial chiral metamaterials have demonstrated extraordinary rotational ability by engineering intra-molecular couplings. However, while in general, chiral metamaterials can exhibit strong rotatory power at or around resonances, they convert linearly polarized waves into elliptically polarized ones. Here, we demonstrate that strong inter-molecular coupling through a small gap between adjacent chiral metamolecules can lead to a broadband enhanced rotating ability with pure rotation of linearly polarized electromagnetic waves. Strong inter-molecular coupling leads to nearly identical behaviour in magnitude, but engenders substantial difference in phase between transmitted left and right-handed waves. PMID:25209452

Kim, Teun-Teun; Oh, Sang Soon; Park, Hyun-Sung; Zhao, Rongkuo; Kim, Seong-Han; Choi, Wonjune; Min, Bumki; Hess, Ortwin

2014-01-01

352

Intermolecular disulfide bonds link specific high-molecular-weight glutenin subunits in wheat endosperm.  

PubMed

A detergent wash extracted soluble proteins from wheat flour, leaving a residue enriched with insoluble glutenin aggregates. Digestion of this residue with endoproteinase Lys-C, which showed a limited specificity for glutenin subunits, produced several peptides with apparent molecular weights close to those of intact high-molecular-weight glutenin subunits. N-terminal sequencing indicated that the isolated peptides were composed of high-molecular-weight glutenin subunit fragments joined by an intermolecular disulfide bond. In two of these peptides, only two components were found, one from an x-type subunit and the other from a y-type subunit. The isolated peptides all contained at least one x-type C-terminal region and one y-type N-terminal region, suggesting a specific orientation to the intermolecular disulfide linkage. PMID:1390908

Tao, H P; Adalsteins, A E; Kasarda, D D

1992-09-01

353

Argentophilic interactions.  

PubMed

The decade 1990-2000 saw a growing interest in aurophilic interactions in gold chemistry. These interactions were found to influence significantly a variety of structural and other physical characteristics of gold(I) compounds. The attention paid to this unusual and counterintuitive type of intra- and intermolecular bonding between seemingly closed-shell metal centers has rapidly been extended to also include silver chemistry. Hundreds of experimental and computational studies have since been dedicated to the argentophilicity phenomenon. The results of this development are reviewed herein focusing on molecular systems where two or more silver(I) centers are in close contact leading to specific structural characteristics and a variety of novel physical properties. These include strongly modified ligand-to-metal charge-transfer processes observed in absorption and emission spectroscopy, but also colossal positive and negative thermal expansion on the one hand and unprecedented negative linear compressibility of crystal parameters on the other. PMID:25393553

Schmidbaur, Hubert; Schier, Annette

2015-01-12

354

Interaction between polymer constituents and the structure of biopolymers  

NASA Technical Reports Server (NTRS)

The paper reviews the current status of methods for calculating intermolecular interactions between biopolymer units. The nature of forces contributing to the various domains of intermolecular separations is investigated, and various approximations applicable in the respective regions are examined. The predictive value of current theory is tested by establishing a connection with macroscopic properties and comparing the theoretical predicted values with those derived from experimental data. This has led to the introduction of a statistical model describing DNA.

Rein, R.

1974-01-01

355

Bull. Liais. Groupe Polyphnols Vol.15, 332-335 (1990). AN ADDITIONAL ASPECT OF INTERMOLECULAR  

E-print Network

-glycosides, intermolecular co-pigmentation, elderberries (sambucus nigra), solid state 13C-NMR (CP/MAS). ABSTRACT Due-pigmentation of cyanin, thus suggesting the formation of a 1:1 complex. In addition, solid state 13C-NMR spectra (CP-500A dichrograph and solid state 13C-NMR spectra (CP/MAS) on a Varian VXR-300 spectrometer at 75

Rüedi, Peter

356

Intermolecular and intramolecular isotope effects in the deamination of putrescine catalyzed by diamine oxidase  

Microsoft Academic Search

Summary The enzymatic deamination of 1,4-diaminobutane (putrescine) catalyzed by hog kidney diamine oxidase was studied with the aid of deuterium labeled substrates and mass spectrometry. An intermolecular deuterium isotope effect for the deamination of putrescine labeled with deuterium in all 4 alpha positions was observed to be 1.26. 1,4-Diaminobutane-1, 1-d2 was synthesized and intramolecular isotope effects determined. The preference of

P. S. Callery; M. S. B. Nayar; E. M. Jakubowski; M. Stogniew

1982-01-01

357

Intermolecular pair potentials and the second virial coefficient of sulphur dioxide vapour  

NASA Astrophysics Data System (ADS)

We have calculated the second virial coefficient of SO 2 for all published intermolecular pair potentials. The main result is that the effective potentials obtained by the molecular dynamics simulation method, with parameters fitted to liquid-state properties of SO 2, give in general reasonable agreement with experiment. The most sophisticated potential, with three Lennard-Jones sites plus experimental dipole and quadrupole moments located at the molecular center of mass, gives good results even in the low-temperature range.

Sokoli?, Franjo; Guissani, Yves; Baranovi?, Goran

1986-11-01

358

Observation and characterization of intermolecular homonuclear single-quantum coherences in liquid nuclear magnetic resonance  

Microsoft Academic Search

Intermolecular zero-quantum and double-quantum coherences (iZQCs and iDQCs) are frequently discussed in literature since they may provide novel contrast mechanisms in magnetic resonance imaging and possibilities for high-resolution spectra in an inhomogeneous and unstable magnetic field. In a previous paper [J. Chem. Phys. 115, 10769 (2001)], we have studied both theoretically and experimentally the properties of iZQC and iDQC nuclear

Zhong Chen; Zhiwei Chen; Jianhui Zhong

2002-01-01

359

Halodiazophosphonates, a new class of diazo compounds for the diastereoselective intermolecular Rh(II) catalyzed cyclopropanation.  

PubMed

(Halodiazomethyl)phosphonates 2A-C have been generated by a one-pot procedure via a clean, efficient, and rapid deprotonation/electrophilic halogenation sequence from diethyl diazomethylphosphonate 1 (EDP). Subsequent intermolecular Rh(II)-catalyzed cyclopropanation afforded the corresponding halocyclopropylphosphonates 3-10 in moderate to high yields and high diastereomeric ratios. Catalyst loadings down to 0.1 mol % as well as clean and selective product formation were achieved. PMID:22616915

Schnaars, Christian; Hansen, Tore

2012-06-01

360

Intra- and inter-molecular photoexcitations in a cyano-substituted poly( p-phenylenevinylene)  

NASA Astrophysics Data System (ADS)

We report a study of time-resolved photoluminescence (PL) in a cyano-substituted poly( p-phenylenevinylene). We have investigated the effect of excitation and emission wavelength as well as solvent on the PL. We observe evidence of luminescence from both intra- and inter-molecular photoexcitations. We find that the relative amounts of these excitations depend strongly on the excitation wavelength and solvent mixture used.

Samuel, I. D. W.; Rumbles, G.; Collison, C. J.; Moratti, S. C.; Holmes, A. B.

1998-02-01

361

Evaluation of glycerol intermolecular free lengths at different temperatures by a thermo-acoustic approach  

NASA Astrophysics Data System (ADS)

The mean intermolecular free length in glycerol is estimated over a wide range of temperatures by making use of thermo-acoustical parameters followed by measurements of glycerol surface tension. To achieve this objective, the glycerol surface tension is measured by using video digital image processing techniques to extract the entire experimental drop profile with subsequent numerical procedures based upon the Laplace equation of capillarity. Glycerol surface tension measurements are extended from 10°C - 90°C with a step of 10°C. The developed model for the evaluation of the glycerol intermolecular free length requires the estimate of the glycerol internal pressure which is derived, in this study, from the Tait equation by exploiting the glycerol nonlinearity parameter and further glycerol properties already measured in a previous study. The experimental results show that the mean intermolecular free length increases, with rise in temperature, from a small value. Inversely, the internal pressure decreases by increasing temperature which describes perfectly the dispersion part of cohesion and reflects the molecular ordering of glycerol versus temperature.

Khelladi, Hassina; Plantier, Frédéric; Daridon, Jean Luc

2012-05-01

362

Entanglement elasticity in polymer chain melts: microscopic calculation of the rubbery plateau modulus via intermolecular correlations  

NASA Astrophysics Data System (ADS)

Textbook models of stress relaxation in melts of entangled polymer chains are built on the assumption that intra-molecular or backbone stresses are the dominant contribution to the system's total stress. Numerous simulations over the last two decades have challenged this assumption, but calculating the intermolecular or non-bonded contribution to the stress has proven a daunting theoretical task. Building on our recent progress in microscopically constructing the transverse confinement field of entangled rods (PRL 107, 078102 (2011)) and ideal coils (PRL 109, 168306 (2012)), we explicitly separate stress correlations into intra- and inter-molecular terms, and calculate the contribution of intermolecular stress correlations in the ``plateau'' region of stress relaxation. We derive, with no adjustable parameters, the characteristic relation Ge˜kBT/p^3 (where p is the packing length) with a prefactor that agrees within a factor of two with experiment and simulation. This theoretical advance has major implications for the effect of nonlinear deformation, confinement, and chain orientational ordering on entanglement elasticity.

Sussman, Daniel; Schweizer, Ken

2013-03-01

363

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids.  

PubMed

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA)(2)] and [(o-TOL)(CA)(2)] have been prepared. The (13)C NMR, (1)H NMR, (1)H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H?N intermolecular hydrogen bond between 2NH(2) groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic. PMID:21531618

Refat, Moamen S; Saad, Hosam A; Adam, Abdel Majid A

2011-08-01

364

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids  

NASA Astrophysics Data System (ADS)

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA) 2] and [(o-TOL)(CA) 2] have been prepared. The 13C NMR, 1H NMR, 1H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH 2 groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic.

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2011-08-01

365

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

PubMed

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

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

2012-07-19

366

Insights into hydrogen bonding via ice interfaces and isolated water  

NASA Astrophysics Data System (ADS)

Water in a confined environment has a combination of fewer available configurations and restricted mobility. Both affect the spectroscopic signature. In this work, the spectroscopic signature of water in confined environments is discussed in the context of competing models for condensed water: (1) as a system of intramolecular coupled molecules or (2) as a network with intermolecular dipole-dipole coupled O-H stretches. Two distinct environments are used: the confined asymmetric environment at the ice surface and the near-isolated environment of water in an infrared transparent matrix. Both the spectroscopy and the environment are described followed by a perspective discussion of implications for the two competing models. Despite being a small molecule, water is relatively complex; perhaps not surprisingly the results support a model that blends inter- and intramolecular coupling. The frequency, and therefore the hydrogen-bond strength, appears to be a function of donor-acceptor interaction and of longer-range dipole-dipole alignment in the hydrogen-bonded network. The O-H dipole direction depends on the local environment and reflects intramolecular O-H stretch coupling.

Shultz, Mary Jane; Bisson, Patrick; Vu, Tuan Hoang

2014-11-01

367

Insights into hydrogen bonding via ice interfaces and isolated water.  

PubMed

Water in a confined environment has a combination of fewer available configurations and restricted mobility. Both affect the spectroscopic signature. In this work, the spectroscopic signature of water in confined environments is discussed in the context of competing models for condensed water: (1) as a system of intramolecular coupled molecules or (2) as a network with intermolecular dipole-dipole coupled O-H stretches. Two distinct environments are used: the confined asymmetric environment at the ice surface and the near-isolated environment of water in an infrared transparent matrix. Both the spectroscopy and the environment are described followed by a perspective discussion of implications for the two competing models. Despite being a small molecule, water is relatively complex; perhaps not surprisingly the results support a model that blends inter- and intramolecular coupling. The frequency, and therefore the hydrogen-bond strength, appears to be a function of donor-acceptor interaction and of longer-range dipole-dipole alignment in the hydrogen-bonded network. The O-H dipole direction depends on the local environment and reflects intramolecular O-H stretch coupling. PMID:25399186

Shultz, Mary Jane; Bisson, Patrick; Vu, Tuan Hoang

2014-11-14

368

Rotational diffusion and intermolecular collisions of a spin labeled alpha-helical peptide determined by electron spin echo spectroscopy.  

PubMed Central

Short peptides that are composed mainly of alanine have recently been shown to form alpha-helices in aqueous solution at low temperature (Marqusee, S., and R. L. Baldwin. 1987. Proc. Natl. Acad. Sci. 84:8898-8902; Marqusee, S., V. H. Robbins, and R. L. Baldwin. 1989. Proc. Natl. Acad. Sci. USA. 86:5286-5290). These peptides are excellent models for probing structure and dynamics in isolated helical domains. In previous work we have designed and synthesized spin labeled analogs of these helix-forming peptides and we have shown that these analogs retain the folding characteristics of the parent peptide (Todd, A. P., and G. L. Millhauser. 1991. Biochemistry. 30:5515-5523). Using conventional continuous wave electron spin resonance (CW ESR) we have further shown that local motion is more pronounced near the helix amino terminus than in the central region as the peptide is thermally unfolded (Miick, S. M., A. P. Todd, and G. L. Millhauser. 1991. Biochemistry. 30:9498-9503). In this present work we use electron spin echo (ESE) spectroscopy to further refine our understanding of the solution dynamics of the 3K-8 peptide, which is a 16-mer with a nitroxide spin label attached at position 8. We find that the spin echo decays are well described by a single exponential function and that the determined correlation times are close to those previously derived from CW experiments. Variable concentration ESE experiments have directly revealed Heisenberg spin exchange (HSE) interactions and we find that the interpeptide collision rate is near to that expected for a free species in solution. This provides strong evidence that the helical conformation of these peptides is not stabilized by intermolecular interactions. PMID:1420935

Miick, S. M.; Millhauser, G. L.

1992-01-01

369

Preparation and magnetic properties of Mn12 clusters with 4-cyanobenzenecarboxylate ligand, [Mn12O12(O2CC6H4-p-CN)16(H2O)4] and its tetraphenylphosphonium salts  

NASA Astrophysics Data System (ADS)

The new Mn12 magnetic clusters with 4-cyanobenzenecarboxylate ligand, [Mn12O12(O2CC6H4-p-CN)16(H2O)4] (1) and its singly (2) and doubly (3) reduced analogs as their tetraphenylphosphonium salts, have been synthesized and characterized by elemental analyses, Raman, ESI-MS spectra and magnetic measurements with a SQUID magnetometer. Unlike the known Mn12 oxocarboxylate clusters, which are very soluble in CH3CN or CH2Cl2, the complex 1 is not dissolved in organic solvents providing an indication for strong intermolecular interactions which lead to strong dipole-dipole interactions between clusters and affect the magnetic behavior. The one-electron and two-electron reduced clusters (2, 3) contain the bulk counterion and dissolve in CH3CN. They show magnetic properties characteristic for anion Mn12 single-molecule magnets.

Sasnovskaya, V. D.; Kushch, L. A.; Yagubskii, E. B.; Sulimenkov, I. V.; Kozlovskiy, V. I.; Zagaynova, V. S.; Makarova, T. L.

2012-09-01

370

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

SciTech Connect

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

Hobbs, M.L.

1997-12-01

371

Direct measurement of the intermolecular forces confining a single molecule in an entangled polymer solution  

E-print Network

We use optical tweezers to directly measure the intermolecular forces acting on a single polymer imposed by surrounding entangled polymers (115 kbp DNA, 1 mg/ml). A tube-like confining field was measured in accord with the key assumption of reptation models. A time-dependent harmonic potential opposed transverse displacement, in accord with recent simulation findings. A tube radius of 0.8 microns was determined, close to the predicted value (0.5 microns). Three relaxation modes (~0.4, 5 and 30 s) were measured following transverse displacement, consistent with predicted relaxation mechanisms.

Rae M. Robertson; Douglas E. Smith

2007-06-25

372

Kinetic Resolution of Racemic Amino Alcohols through Intermolecular Acetalization Catalyzed by a Chiral Brønsted Acid.  

PubMed

The kinetic resolution of racemic secondary alcohols is a fundamental method for obtaining enantiomerically enriched alcohols. Compared to esterification, which is a well-established method for this purpose, kinetic resolution through enantioselective intermolecular acetalization has not been reported to date despite the fact that the formation of acetals is widely adopted to protect hydroxy groups. By taking advantage of the thermodynamics of acetalization by the addition of alcohols to enol ethers, a highly efficient kinetic resolution of racemic amino alcohols was achieved for the first time and in a practical manner using a chiral phosphoric acid catalyst. PMID:25581575

Yamanaka, Takuto; Kondoh, Azusa; Terada, Masahiro

2015-01-28

373

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

PubMed Central

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

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

2014-01-01

374

Catalytic asymmetric synthesis of 8-oxabicyclooctanes by intermolecular [5+2] pyrylium cycloadditions.  

PubMed

Highly enantioselective intermolecular [5+2] cycloadditions of pyrylium ion intermediates with electron-rich alkenes are promoted by a dual catalyst system composed of an achiral thiourea and a chiral primary aminothiourea. The observed enantioselectivity is highly dependent on the substitution pattern of the 5? component, and the basis for this effect is analyzed using experimental and computational evidence. The resultant 8-oxabicyclo[3.2.1]octane derivatives possess a scaffold common in natural products and medicinally active compounds and are also versatile chiral building blocks for further manipulations. Several stereoselective complexity-generating transformations of the 8-oxabicyclooctane products are presented. PMID:24782332

Witten, Michael R; Jacobsen, Eric N

2014-06-01

375

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

376

The variation of viscosity, refractive indices, compressibility, intermolecular free length, and excess molar volume of the acetophenone—ethyl acetate solutions at 303.15-323.15 K  

NASA Astrophysics Data System (ADS)

Densities, viscosities, refractive indices and ultrasonic velocities of the binary mixtures of acetophenone with ethyl acetate were measured over the entire mole fractions at 303.15, 313.15, and 323.15 K. From the experimental results, excess molar volumes V E, viscosity deviation ??, refractive index deviation ? n D , deviations in isentropic compressibility ?? s and excess intermolecular free length ? L f are calculated. The viscosity values were fitted to the models of Krishnan-Laddha and McAllister. The thermophysical properties under study were fit to the Jouyban-Acree model. The excess values were correlated using Redlich-Kister polynomial equation to obtain their coefficients and standard deviations. The data obtained fitted with the values correlated by the corresponding models very well. The results are interpreted in terms of molecular interactions occurring in the solution.

Saravanakumar, K.; Baskaran, R.; Kubendran, T. R.

2012-12-01

377

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

NASA Astrophysics Data System (ADS)

Femtosecond pump probe spectroscopy was employed to measure intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) of benzene in the gas phase and in supercritical (sc) CO 2. We observe two IVR time scales the faster of which proceeds within ? IVR(1)<0.5 ps. The slower IVR component has a time constant of ? IVR(2)=(48±5) ps in the gas phase and in scCO 2 is accelerated by interactions with the solvent. At the highest CO 2 density it is reduced to ? IVR(2)=(6±1) ps. The corresponding IVR rate constants show a similar density dependence as the VET rate constants. Model calculations suggest that both quantities correlate with the local CO 2 density in the immediate surrounding of the benzene molecule.

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

2004-03-01

378

Novel Pressure-Induced Interactions in Silane-Hydrogen  

SciTech Connect

We report novel molecular compound formation from silane-hydrogen mixtures with intermolecular interactions unprecedented for hydrogen-rich solids. A complex H2 vibron spectrum with anticorrelated pressure-frequency dependencies and a striking H-D exchange below 10 GPa reveal strong and unusual attractive interactions between SiH4 and H2 and molecular bond destabilization at remarkably low pressure. The unique features of the observed SiH4(H2)2 compound suggest a new range of accessible pressure-driven intermolecular interactions for hydrogen-bearing simple molecular systems and a new approach to perturb the hydrogen covalent bond.

Strobel, T.; Somayazulu, M; Hemley, R

2009-01-01

379

Foot-and-mouth disease virus leader proteinase: structural insights into the mechanism of intermolecular cleavage.  

PubMed

Translation of foot-and-mouth disease virus RNA initiates at one of two start codons leading to the synthesis of two forms of leader proteinase L(pro) (Lab(pro) and Lb(pro)). These forms free themselves from the viral polyprotein by intra- and intermolecular self-processing and subsequently cleave the cellular eukaryotic initiation factor (eIF) 4 G. During infection, Lb(pro) removes six residues from its own C-terminus, generating sLb(pro). We present the structure of sLb(pro) bound to the inhibitor E64-R-P-NH2, illustrating how sLb(pro) can cleave between Lys/Gly and Gly/Arg pairs. In intermolecular cleavage on polyprotein substrates, Lb(pro) was unaffected by P1 or P1' substitutions and processed a substrate containing nine eIF4GI cleavage site residues whereas sLb(pro) failed to cleave the eIF4GI containing substrate and cleaved appreciably more slowly on mutated substrates. Introduction of 70 eIF4GI residues bearing the Lb(pro) binding site restored cleavage. These data imply that Lb(pro) and sLb(pro) may have different functions in infected cells. PMID:25240326

Steinberger, Jutta; Grishkovskaya, Irina; Cencic, Regina; Juliano, Luiz; Juliano, Maria A; Skern, Tim

2014-11-01

380

Intermolecular association between caspase-mediated cleavage fragments of phospholipase D1 protects against apoptosis.  

PubMed

Phospholipase D plays an anti-apoptotic role but little is known about dynamics of phospholipase D turnover during apoptosis. We have recently identified phospholipase D1 as a new substrate of caspases which generates the N-terminal and C-terminal fragment of phospholipase D1. In the present study, we tried to investigate whether association of the caspase cleavage fragments may be involved in regulation of apoptosis. Ectopically expressed C-terminal fragment, but not N-terminal fragment of phospholipase D1, is exclusively imported into the nucleus via a nuclear localization sequence; however, endogenous C-terminal fragment of phospholipase D1 from etoposide-induced apoptotic cells and Alzheimer's disease brain tissues with active caspase-3, was localized in the cytosolic fraction as well as the nuclear fraction. Intermolecular association between the two fragments of phospholipase D1 through hydrophobic residues within the catalytic motif inhibited nuclear localization of C-terminal fragment of phospholipase D1, and two catalytic motif and nuclear localization sequence regulated nuclocytoplasmic shuttling of phospholipase D1. Moreover, hydrophobic residues involved in the intermolecular association are also required for both its enzymatic activity and anti-apoptotic function. Taken together, we demonstrate that interdomain association and dissociation of phospholipase D1 might provide new insights into modulation of apoptosis. PMID:22108201

Jang, Young Hoon; Min, Do Sik

2012-02-01

381

New infrared bands of nonpolar OCS dimer and experimental frequencies for two intermolecular modes  

NASA Astrophysics Data System (ADS)

Spectra of the nonpolar carbonyl sulfide dimer in the region of the OCS ?1 fundamental band were observed in a slit-jet supersonic expansion. The jet was probed using radiation from a tunable diode laser employed in a rapid-scan signal averaging mode. Six new bands were observed and analyzed, all of which originate from the dimer ground vibrational state. Three were vibrational fundamentals involving the (18OCS)2 and 16OCS-18OCS isotopologues. They enabled an estimate to be made of the frequency of the infrared-forbidden mode corresponding to in-phase vibration of the OCS monomers in the dimer, a value needed to obtain an intermolecular vibrational frequency from one of the observed combination bands. A relatively weak b-type dimer band centered at 2103.105 cm-1 was assigned to the OCS 4?2 (l = 0) bending overtone. Combination bands were observed involving the geared bend and van der Waals stretch intermolecular modes. The resulting experimental frequencies of 37.5(20) cm-1 for the bend and 42.9727(1) cm-1 for the stretch are in good agreement with a recent high level theoretical calculation.

Afshari, M.; Dehghany, M.; McKellar, A. R. W.; Moazzen-Ahmadi, N.

2012-08-01

382

New infrared bands of nonpolar OCS dimer and experimental frequencies for two intermolecular modes.  

PubMed

Spectra of the nonpolar carbonyl sulfide dimer in the region of the OCS ?(1) fundamental band were observed in a slit-jet supersonic expansion. The jet was probed using radiation from a tunable diode laser employed in a rapid-scan signal averaging mode. Six new bands were observed and analyzed, all of which originate from the dimer ground vibrational state. Three were vibrational fundamentals involving the ((18)OCS)(2) and (16)OCS-(18)OCS isotopologues. They enabled an estimate to be made of the frequency of the infrared-forbidden mode corresponding to in-phase vibration of the OCS monomers in the dimer, a value needed to obtain an intermolecular vibrational frequency from one of the observed combination bands. A relatively weak b-type dimer band centered at 2103.105 cm(-1) was assigned to the OCS 4?(2) (l = 0) bending overtone. Combination bands were observed involving the geared bend and van der Waals stretch intermolecular modes. The resulting experimental frequencies of 37.5(20) cm(-1) for the bend and 42.9727(1) cm(-1) for the stretch are in good agreement with a recent high level theoretical calculation. PMID:22894345

Afshari, M; Dehghany, M; McKellar, A R W; Moazzen-Ahmadi, N

2012-08-01

383

Conformational diversity in prion protein variants influences intermolecular [beta]-sheet formation  

SciTech Connect

A conformational transition of normal cellular prion protein (PrP{sup C}) to its pathogenic form (PrP{sup Sc}) 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 {beta}-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 {beta}-sheets involving the M/V129 polymorphic residue.

Lee, Seungjoo; Antony, Lizamma; Hartmann, Rune; Knaus, Karen J.; Surewicz, Krystyna; Surewicz, Witold K.; Yee, Vivien C. (Case Western); (Cleveland Clinic)

2010-04-19

384

Theoretical studies of molecular interactions  

SciTech Connect

This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

Lester, W.A. Jr. [Univ. of California, Berkeley (United States)

1993-12-01

385

Electrohydrodynamic interaction of spherical particles under Quincke rotation  

NASA Astrophysics Data System (ADS)

Weakly conducting dielectric particles suspended in a dielectric liquid of higher conductivity can undergo a transition to spontaneous sustained rotation when placed in a sufficiently strong dc electric field. This phenomenon of Quincke rotation has interesting implications for the rheology of these suspensions, whose effective viscosity can be controlled and reduced by application of an external field. While previous models based on the rotation of isolated particles have provided accurate estimates for this viscosity reduction in dilute suspensions, discrepancies have been reported in more concentrated systems where particle-particle interactions are likely significant. Motivated by this observation, we extend the classic description of Quincke rotation based on the Taylor-Melcher leaky dielectric model to account for pair electrohydrodynamic interactions between two identical spheres using the method of reflections. A coupled system of evolution equations for the dipole moments and angular velocities of the spheres is derived that accounts for electric dipole-dipole interactions and hydrodynamic rotlet interactions up to order O(R-5), where R is the separation distance between the spheres. A linear stability analysis of this system shows that interactions modify the value of the critical electric field for the onset of Quincke rotation: both electric and hydrodynamic interactions can either stabilize or destabilize the system depending on the orientation of the spheres, but the leading effect of interactions on the onset of rotation is hydrodynamic. We also analyze the dynamics in the nonlinear regime by performing numerical simulations of the governing equations. In the case of a pair of spheres that are fixed in space, we find that particle rotations always synchronize in magnitude at long times, though the directions of rotation of the spheres need not be the same. The steady-state angular velocity magnitude depends on the configuration of the spheres and electric field strength and agrees very well with an asymptotic estimate derived for corotating spheres. In the case of freely-suspended spheres, dipolar interactions are observed to lead to a number of distinct behaviors depending on the initial relative configuration of the spheres and on any infinitesimal initial perturbation introduced in the system: in some cases the spheres slowly separate in space while steadily rotating, while in other cases they pair up and either corotate or counterrotate depending on their orientation relative to the field.

Das, Debasish; Saintillan, David

2013-04-01

386

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

Microsoft Academic Search

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

R. Nigel Edwards

1997-01-01

387

Report on dipole-dipole resistivity and technology transfer at the Ahuachapan Geothermal field Ahuachapan, El Salvador  

SciTech Connect

The Ahuachapan Geothermal Field (AGF) is a 90 megawatt geothermal-sourced powerplant operated by the Comision Ejecutiva Hidroelectrica del Rio Lempa (CEL) of El Salvador. During the period November 1987 through May 1988 a deep resistivity survey and technology transfer was performed at the AGF at the request of Los Alamos National Laboratory (LANL) as part of a United States Agency for International Development (USAID) project. The resistivity surveying is ongoing at the time of this report under the supervision of CEL personnel. LANL and contract personnel were present at the site during performance of the initial surveying for the purpose of technology transfer. This report presents the results and interpretation of the two initial resistivity survey lines performed on site during and shortly after the technology transfer period.

Fink, J.B. (Geophynque International, Tucson, AZ (United States))

1988-08-01

388

Optoelectronic method for analysis of biomolecular interaction dynamics  

NASA Astrophysics Data System (ADS)

Optoelectronic method of laser correlation spectroscopy for study of intermolecular interaction in biomolecular suspension is presented. The method of laser correlation spectroscopy is integrated with orthogonal laser light scattering and ultramicroscopy technique for visual control of biomolecular interactions. The capabilities of the method for analysis of biomolecular conglomerates dynamics are considered.

Nepomnyashchaya, E.; Velichko, E.; Aksenov, E.; Bogomaz, T.

2014-10-01

389

Ordered and layered structure of liquid nitromethane within a graphene bilayer: toward stabilization of energetic materials through nanoscale confinement.  

PubMed

The structural characteristics involving thermal stabilities of liquid nitromethane (NM)-one of the simplest energetic materials-confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and layered structures are formed at the confinement of the GRA bilayer induced by the van der Waals attractions of NM with GRA and the dipole-dipole interactions of NM, which is strongly dependent on the confinement size, i.e., the GRA bilayer distance. These unique intermolecular arrangements and preferred orientations of confined NM lead to higher stabilities than bulk NM revealed by bond dissociation energy calculations. PMID:25672840

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Kang, Ying; Ge, Zhongxue

2015-03-01

390

Calculations of structure and IR-spectrum for small UF6 clusters  

NASA Astrophysics Data System (ADS)

A new site-site intermolecular potential model for UF6, featuring exchange, dispersion, electrostatic and induction terms, is presented. The new potential, with the parameters adjusted according to the observed monomer transition dipole moment and reproducing the experimental temperature dependence of the second virial coefficient, is used to determine UF6 cluster structures up to the hexamer and, by means of a second order line shift formalism, to calculate the corresponding IR-spectra in the region of the ?3 vibrational mode (at 627.724 cm-1). The contributions of the various potential terms to the frequency shifts are analyzed and the leading interaction mechanism is found to be the resonant dipole-dipole coupling. The theoretical spectra are compared and interpreted against recent Fourier transform IR-spectroscopy measurements.

Beu, T. A.; Onoe, J.; Takeuchi, K.

1997-04-01

391

Temperature dependence of the triplet diffusion and quenching rates in films of an Ir(ppy)3 -cored dendrimer  

NASA Astrophysics Data System (ADS)

We study photoluminescence and triplet-triplet exciton annihilation in a neat film of a fac-tris(2-phenylpyridyl)iridium(III) [Ir(ppy)3] -cored dendrimer and in its blend with a 4,4' -bis( N -carbazolyl)biphenyl host for the temperature range of 77-300K . The nearest neighbor hopping rate of triplet excitons is found to increase by a factor of 2 with temperature between 150 and 300K and is temperature independent at lower temperature. The intermolecular quenching rate follows the Arrhenius law with an activation energy of 7meV , which can be explained by stronger dipole-dipole interactions with the donor molecule in the higher triplet substate. The results indicate that energy disorder has no significant effect on triplet transport and quenching in these materials.

Ribierre, J. C.; Ruseckas, A.; Samuel, I. D. W.; Staton, S. V.; Burn, P. L.

2008-02-01

392

Controlling Er-Tm interaction in Er and Tm codoped silicon-rich silicon oxide using nanometer-scale spatial separation for efficient, broadband infrared luminescence  

SciTech Connect

The effect of nanometer-scale spatial separation between Er{sup 3+} and Tm{sup 3+} ions in Er and Tm codoped silicon-rich silicon oxide (SRSO) films is investigated. Er and Tm codoped SRSO films, which consist of nanocluster Si (nc-Si) embedded inside SiO{sub 2} matrix, were fabricated with electron cyclotron resonance-plasma enhanced chemical vapor deposition of SiH{sub 4} and O{sub 2} with concurrent sputtering of Er and Tm metal targets. Spatial separation between Er{sup 3+} and Tm{sup 3+} ions was achieved by depositing alternating layers of Er- and Tm-doped layers of varying thickness while keeping the total film thickness the same. The films display broadband infrared photoluminescence (PL) from 1.5 to 2.0 {mu}m under a single source excitation due to simultaneous excitation of Er{sup 3+} and Tm{sup 3+} ions by nc-Si. Increasing the layer thickness from 0 to 72 nm increases the Er{sup 3+} PL intensity nearly 50-fold while the Tm{sup 3+} PL intensity is unaffected. The data are well-explained by a model assuming a dipole-dipole interaction between excited Er{sup 3+} and Tm{sup 3+} ions, and suggest that by nanoscale engineering, efficient, ultrabroadband infrared luminescence can be obtained in an optically homogeneous material using a single light source.

Seo, Se-Young; Shin, Jung H. [Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 373-1 Guseong-dong, Yuseong-gu, Daejon (Korea, Republic of)

2004-11-01

393

A study of palladium catalyzed intra/intermolecular cascade cross coupling/cyclizations involving bicyclopropylidene.  

PubMed

The compounds [3-(2-Bromocyclohex-2-enyloxy)prop-1-ynyl]-tert-butyl-dimethylsilane 3, [4-(2-bromocyclohex-2-en-1-yloxy)but-2-yn-1-yloxy]tert-butyldimethylsilane 5 and dimethyl 2-(2-bromocyclohex-2-enyl)-2-(3-(tert-butyldimethylsilanyl)prop-2-ynyl)malonate 9 were prepared and subjected to palladium-catalyzed intra-intermolecular cascade cross couplings incorporating bicyclopropylidene 10 under two types of conditions. In the presence of Pd(OAc)2, PPh3 and K2CO3 in acetonitrile at 80 °C, the products were indene analogues, cross-conjugated tetraenes 11, 12 and 13, respectively. The corresponding spirocyclopropanated tricycle 16 in dimethylformamide at 110 °C was obtained, albeit in low yield (24%), and observed as an equimolar mixture of diastereomers, whereas 14, 15 were not fully isolated. PMID:24828378

Demircan, Aydin

2014-01-01

394

Influence of intermolecular hydrogen bonds on the luminescence properties of {alpha}-substituted cinnamonitriles  

SciTech Connect

In view of the dramatic difference in the spectral-luminescence properties of {alpha}-(p-chlorobenzoyl)-4-diethylaminocinnamonitrile and {alpha}-ethoxycarbonyl-4-diethylaminocinnamonitrile in solutions and in the crystalline state, X-ray diffraction analysis has been applied to study crystals of these compounds. The intermolecular C-H...N and C-H...O hydrogen bonds are found to contribute to the quinoidization of molecules, which leads to a bathochromic shift in the absorption and fluorescence spectra. A spectral-luminescence study of the aforementioned compounds has revealed that the solvent temperature and polarity affect the position of absorption and luminescence peaks: a decrease in these parameters causes a hypsochromic shift.

Mikhlina, Ya. A.; Bolotin, B. M., E-mail: bolotin70@yandex.ru [State Research Institute of Chemical Reagents and Especially Pure Chemical Substances (Russian Federation); Uzhinov, B. M., E-mail: uzhinov@light.chem.msu.ru; Volchkov, V. V. [Moscow State University, Faculty of Chemistry (Russian Federation)] [Moscow State University, Faculty of Chemistry (Russian Federation); Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

2013-03-15

395

Correlation of transducin photoaffinity labeling with the specific formation of intermolecular disulfide linkages in its ?-subunit.  

PubMed

Transducin (T) is a heterotrimer of T?, T?, and T? subunits. In the presence of light-activated rhodopsin, 8-azidoguanosine triphosphate (8-N3GTP) was covalently incorporated into T in a UV-light photodependent manner, with a low stoichiometry of 0.02 mol of 8-N3GTP per mol of T. Although T? was preferentially labeled by 8-N3GTP, T? and T? were also modified. Photolabeling of T was specifically inhibited by GDP and GTP, but not by ?,?-imido-guanosine 5'-triphosphate (GMP-PNP), indicating that 8-N3GTP was modifying the GDP binding site of the holoenzyme. This was consistent with the observation that the photoaffinity probe was completely hydrolyzed to 8-N3GDP by T activated by illuminated rhodopsin. The formation of intermolecular disulfide associations in T was also determined because photolabeling of T was performed under non-reducing conditions. We established that Cys-347 of T? was the major residue involved in the formation of disulfide-linked T oligomers. Other cysteines of T?, such as Cys-321, also participated in the formation of disulfide bonds, revealing a complex pattern of intermolecular disulfide cross-links that led to the polymerization of T. The spontaneous generation of these cystines in T? inhibited the light-dependent GTPase and GMP-PNP binding activities of T. A model was constructed illustrating that when two heterotrimers dimerize through the formation of disulfide bridges between the Cys-347 of their T? subunits, the guanine ring of the 8-N3GDP bound to one T molecule might approach to the T??-complex of the other heterotrimer. This model provides an explanation for the additional photolabeling of T? and T? by 8-N3GTP. PMID:25450251

Perdomo, Deisy; Möller, Carolina; Bubis, José

2015-01-01

396

Molecular structures and ? ? interactions of some flavonoids and biflavonoids  

NASA Astrophysics Data System (ADS)

The molecular structures of two flavones, wogonin ( 1) and mikanin ( 2), and two biflavonoids, cupressuflavone ( 3) and neochamaejasmin A ( 4), were determined by single-crystal X-ray analysis. The intermolecular ?-? interactions in 1- 4 and the flavanones alpinetin ( 5) and naringenin ( 6) were investigated. Compounds 1- 4 feature offset face-to-face intermolecular ?-? interactions with centroid-centroid distances ranging from 3.70 to 3.81 Å and displacement angles ranging from 2.7 to 9.9°.

Jiang, Ren-Wang; Ye, Wen-Cai; Woo, Ka-Yan; Du, Jiang; Che, Chun-Tao; But, Paul Pui-Hay; Mak, Thomas C. W.

2002-12-01

397

Far-infrared vibration-rotation-tunneling spectroscopy of Ar-NH3: Intermolecular vibrations and effective angular potential energy surface  

E-print Network

Far-infrared vibration-rotation-tunneling spectroscopy of Ar-NH3: Intermolecular vibrations intermolecular vibration-rotation-tunneling (VRT) bandsof Ar-NH3 havebeen measuredusingtunable far infrared'employeda close-couplingmethod to fit exten- sive far-infrared vibration rotation tunneling (FIR-VRT) spectraof

Cohen, Ronald C.

398

Magneto-Dielectric Effects Induced by Optically-Generated Intermolecular Charge-Transfer States in Organic Semiconducting Materials  

PubMed Central

Traditionally, magneto-dielectric effects have been developed by combining ferroelectric and magnetic materials. Here, we show a magneto-dielectric effect from optically-generated intermolecular charge-transfer states in an organic semiconducting donor:acceptor (PVK:TCNB) system. We observe in magnetic field effects of photoluminescence that a magnetic field can change singlet/triplet population ratio in intermolecular charge-transfer states. Furthermore, our theoretical analysis and experimental evidence indicate that the singlets and triplets in charge-transfer states have stronger and weaker electrical polarizations, respectively. Therefore, the observed magneto-dielectric effect can be attributed to magnetically-dependent singlet/triplet ratio in intermolecular charge-transfer states. In principle, a magneto-dielectric effect can be generated through two different channels based on magneto-polarization and magneto-current effects when the singlet/triplet ratio in intermolecular charge-transfer states is changed by a magnetic field. We find, from the simulation of dielectric effects, that magneto-polarization and magneto-current effects play primary and secondary roles in the generation of magneto-dielectric effect. PMID:24084983

Zang, Huidong; Yan, Liang; Li, Mingxing; He, Lei; Gai, Zheng; Ivanov, Ilia; Wang, Min; Chiang, Long; Urbas, Augustine; Hu, Bin

2013-01-01

399

Terahertz phonon modes of an intermolecular network of hydrogen bonds in an anhydrous ?- d-glucopyranose crystal  

Microsoft Academic Search

First-principles calculations of single molecular vibrations and the crystalline phonons of an anhydrous ?-d-glucopyranose monosaccharide crystal in the terahertz region were performed using periodic density functional theory (DFT) calculations. The calculated frequencies and eigenvectors of the phonon modes, which agreed with experimental results, did not correspond to those of the modes of a single molecule, mainly due to intermolecular hydrogen

Shigeki Saito; Talgat M. Inerbaev; Hiroshi Mizuseki; Nobuaki Igarashi; Yoshiyuki Kawazoe

2006-01-01

400

Gold-Catalyzed Intermolecular Nitrene Transfer from 2H-Azirines to Ynamides: A Direct Approach to Polysubstituted Pyrroles.  

PubMed

An effective gold-catalyzed intermolecular nitrene transfer by the reaction of 2H-azirines and ynamides is reported, which provides highly substituted pyrroles in a straightforward manner. This transformation proceeds under mild conditions and gives the polysubstituted pyrroles in good-to-excellent yields. Preliminary results indicate that a nongold carbenoid pathway is preferred for current pyrrole synthesis. PMID:25514612

Zhu, Lei; Yu, Yinghua; Mao, Zhifeng; Huang, Xueliang

2015-01-01

401

Synthesis of Azepines by a Gold-Catalyzed Intermolecular [4 + 3]-Annulation Nathan D. Shapiro and F. Dean Toste*  

E-print Network

Synthesis of Azepines by a Gold-Catalyzed Intermolecular [4 + 3]-Annulation Nathan D. Shapiro and F 29, 2008; E-mail: fdtoste@berkeley.edu Gold catalysis has recently generated a variety of valuable methods for the synthesis of complex structures from simple starting materials.1 While the majority

Toste, Dean

402

Determination of an improved intermolecular global potential energy surface for Ar-H20 from vibration-rotation-tunneling spectroscopy  

E-print Network

nonlinear least squaresfit to 37 far infrared, infrared, and microwave spectro- scopic measurements.The new infrared VRT spectroscopy-the most direct probe of the details of intermolecular forces-and new nu- merical vibration-rotation-tunneling spectroscopy R. C. Cohena) and R. J. Saykally Department of Chemistry

Cohen, Ronald C.

403

An investigation of three-body effects in intermolecular forces. III. Far infrared laser vibration-rotation-tunneling spectroscopy  

E-print Network

An investigation of three-body effects in intermolecular forces. III. Far infrared laser vibration.2 cm-`, com- pleting the high resolution far infrared measurements of the three lowest-lying Ar by high resolution microwave," far in- frared, l2 and near infraredi spectroscopy. In particular

Cohen, Ronald C.

404

Measurement of the v8 intermolecular vibration of (D,O), by tunable far infrared laser spectroscopy  

E-print Network

Measurement of the v8 intermolecular vibration of (D,O), by tunable far infrared laser spectroscopy the use of tunable far-IR laser spectroscopy of planar super- sonic expansions, as developed, high resolution spectroscopy experiments performed over the past decade have characterized the prop

Cohen, Ronald C.

405

A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Kr-H2O complex.  

PubMed

We report a new three-dimensional ab initio intermolecular potential energy surface for the Kr-H(2)O complex with the H(2)O monomer fixed at its experimental averaged structure. Using the supermolecular approach, the intermolecular potential energies were evaluated at the coupled-cluster singles and doubles level with noniterative inclusion of connected triples with the full counterpoise correction for the basis set superposition error and a large basis set including bond functions. The global minimum corresponding to a planar H-bond configuration was located at the intermolecular distance of 3.82 A? with a well depth of 169.98 cm(-1). In addition, two first-order and one second-order saddle points were also identified. The combined radial discrete variable representation?angular finite basis representation method and the Lanczos algorithm were employed to calculate the rovibrational energy levels for 16 isotopic species of the Kr-H(2)O complexes. The rotational transition frequencies, structure parameters, and nuclear quadrupole coupling constants were also determined for the ground and first intermolecular vibrational excited states and are all in good agreement with the available experimental values. PMID:23249010

Lei, Jinping; Zhou, Yanzi; Xie, Daiqian; Zhu, Hua

2012-12-14

406

A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Kr-H2O complex  

NASA Astrophysics Data System (ADS)

We report a new three-dimensional ab initio intermolecular potential energy surface for the Kr-H2O complex with the H2O monomer fixed at its experimental averaged structure. Using the supermolecular approach, the intermolecular potential energies were evaluated at the coupled-cluster singles and doubles level with noniterative inclusion of connected triples with the full counterpoise correction for the basis set superposition error and a large basis set including bond functions. The global minimum corresponding to a planar H-bond configuration was located at the intermolecular distance of 3.82 Å with a well depth of 169.98 cm-1. In addition, two first-order and one second-order saddle points were also identified. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to calculate the rovibrational energy levels for 16 isotopic species of the Kr-H2O complexes. The rotational transition frequencies, structure parameters, and nuclear quadrupole coupling constants were also determined for the ground and first intermolecular vibrational excited states and are all in good agreement with the available experimental values.

Lei, Jinping; Zhou, Yanzi; Xie, Daiqian; Zhu, Hua

2012-12-01

407

Gold(I)-Catalyzed Intermolecular Addition of Phenols and Carboxylic Acids to Cai-Guang Yang and Chuan He*  

E-print Network

Gold(I)-Catalyzed Intermolecular Addition of Phenols and Carboxylic Acids to Olefins Cai-Guang Yang 60637 Received January 20, 2005; E-mail: chuanhe@uchicago.edu Gold-catalyzed reactions have emerged as important synthetic methods.1 Cationic gold(I) and gold(III) show exceptional activities to activate alkynes

He, Chuan

408

Applications and Analogies: Phototherapy and the Treatment of Hyperbilirubinemia: A Demonstration of Intra- versus Intermolecular Hydrogen Bonding.  

ERIC Educational Resources Information Center

Background information and procedures are provided for a demonstration of intramolecular versus intermolecular hydrogen bonding. The demonstration is based on structural changes in bilirubin molecules which lead to changes in physical properties. A list of further investigations to try is included. (JN)

Wilbraham, Antony C.

1984-01-01

409

Chemistry of the collagen cross-links. Isolation and characterization of two intermediate intermolecular cross-links in collagen  

PubMed Central

This paper describes the isolation from reduced collagen of two new amino acids believed to be involved, in their non-reduced form, as intermolecular cross-links stabilizing the collagen fibre. The reduction of intact collagen fibrils with tritiated sodium borohydride was found to stabilize the aldehyde-mediated cross-links to acid hydrolysis and thus allowed their location and isolation from acid hydrolysates on an automatic amino acid analyser. Comparison of the radioactive elution patterns from the autoanalyser of collagen treated in various ways before reduction permitted a preliminary classification of the peaks into cross-link precursors, intramolecular and intermolecular cross-links. The techniques employed to isolate the purified components on a large scale and to identify them structurally are described in detail. Two labile intermolecular cross-links were isolated in their reduced forms, one of which was identified by high-resolution mass spectrometry as N?-(5-amino-5-carboxypentyl)hydroxylysine. The structure of this compound was confirmed by chemical synthesis. The cross-link precursor ?-aminoadipic ?-semialdehyde was isolated in its reduced form, ?-hydroxynorleucine, together with its acid degradation product ?-chloronorleucine. A relatively stable intermolecular cross-link was isolated and partially characterized by mass spectrometry as an aldol resulting from the reaction of the ?-semialdehyde derived from lysine and hydroxylysine. PMID:5451907

Bailey, A. J.; Peach, Catherine M.; Fowler, L. J.

1970-01-01

410

Intermolecular Packing and Alignment in an Ordered -Hairpin Antimicrobial Peptide Aggregate from 2D Solid-State NMR  

E-print Network

Intermolecular Packing and Alignment in an Ordered -Hairpin Antimicrobial Peptide Aggregate from 2D@iastate.edu Abstract: The aggregation and packing of a membrane-disruptive -hairpin antimicrobial peptide, protegrin-1 in general and for gaining insights into the oligomerization of antimicrobial peptides in lipid bilayers

Hong, Mei

411

Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: Does a stronger acid make a stiffer hydrogen bond?  

NASA Astrophysics Data System (ADS)

Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m-1 for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

Houjou, Hirohiko

2011-10-01

412

Nano-structured complexes of reserpine and quinidine drugs with chloranilic acid based on intermolecular H-bond: spectral and surface morphology studies.  

PubMed

The study of the drug-acceptor interaction may be useful in understanding the drug-receptor interactions and the mechanism of drug action. Here, complexes of reserpine (Res) and quinidine (Qui) drugs with chloranilic acid (CLA) have been synthesized. Then, these complexes were characterized chemically and structurally using CHN elemental analysis, infrared (IR) and electronic absorption spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM). The stoichiometry of the H-bonded complex was found to have a 1:1 ratio, so these complexes can be formulated as [(Drug)(CLA)]. IR measurements confirmed the presence of intermolecular H-bond. Application of Debye-Scherrer equation indicates that the formed complexes are in the range of nano-size. The Res complex exhibits a remarkable crystalline morphology. It was also found that the particle size of Res complex is 1.533 time higher than that of Qui complex. Interestingly, free Res molecular weight is higher than that of free Qui by the same ratio (precisely; 1.525). PMID:24632163

Adam, Abdel Majid A

2014-06-01

413

Nano-structured complexes of reserpine and quinidine drugs with chloranilic acid based on intermolecular H-bond: Spectral and surface morphology studies  

NASA Astrophysics Data System (ADS)

The study of the drug-acceptor interaction may be useful in understanding the drug-receptor interactions and the mechanism of drug action. Here, complexes of reserpine (Res) and quinidine (Qui) drugs with chloranilic acid (CLA) have been synthesized. Then, these complexes were characterized chemically and structurally using CHN elemental analysis, infrared (IR) and electronic absorption spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM). The stoichiometry of the H-bonded complex was found to have a 1:1 ratio, so these complexes can be formulated as [(Drug)(CLA)]. IR measurements confirmed the presence of intermolecular H-bond. Application of Debye-Scherrer equation indicates that the formed complexes are in the range of nano-size. The Res complex exhibits a remarkable crystalline morphology. It was also found that the particle size of Res complex is 1.533 time higher than that of Qui complex. Interestingly, free Res molecular weight is higher than that of free Qui by the same ratio (precisely; 1.525).

Adam, Abdel Majid A.

2014-06-01

414

Reactivity trends of Fe phthalocyanines confined on graphite electrodes in terms of donor-acceptor intermolecular hardness: Linear versus volcano correlations  

NASA Astrophysics Data System (ADS)

In this work, we have studied the interaction between the hydrazine N2H4 molecule with several FeN4 macrocyclic complexes (FePc's). In order to modulate the electron density located on the metal center using iron-phthalocyanine (FePc) as the reference, we used substituted iron-phthalocyanines with different types of substituents electron-donating groups such as iron-tetraamino-phthalocyanine (4?(NH2)FePc) and iron-octamethoxyphthalocyanine (8?(OCH3)FePc), and with electron-withdrawing groups such as iron-tetranitrophthalocyanine(4?(NO2)FePc) and iron-hexadecachlorophthalocyanine (16(Cl)FePc), respectively. We have found that the energy of interaction between hydrazine and the Fe center in the macrocycle increases as the electron-withdrawing power of the substituents increases. When rate constants instead of currents are compared in a semilog plot versus ??D-A, a linear correlation is found where log k increases as the intermolecular hardness of the systems decreases.

Linares-Flores, C.; Espinoza-Vergara, J.; Zagal, J. H.; Arratia-Perez, R.

2014-10-01

415

Effects of intermolecular forces and backbone architecture on the phase behavior of fluorocopolymer-supercritical fluid mixtures  

NASA Astrophysics Data System (ADS)

The impact of polymer backbone architecture on fluorocopolymer solubility in supercritical fluid (SCF) solvents is studied by systematically varying the chemical type of the repeat units in the main chain. The fluorocopolymers investigated include nonpolar copolymers of tetrafluoroethylene with 19 mol% hexafluoropropylene (FEPsb{19}) and 48 mol% hexafluoropropylene (FEPsb{48}) and a polar copolymer of vinylidene fluoride with 22 mol% hexafluoropropylene (Fluorelsp°ler ). The solvents are methodically varied from nonpolar perfluoroalkanes and SFsb6 to polar fluorocarbons and COsb2. Low molecular weight solvents are used to facilitate in interpreting the intermolecular forces that control fluorocopolymer solubility, although pressures in excess of 2,500 bar are sometimes needed to dissolve the fluorocopolymers in these simple solvents. Polarity effects, which vary inversely with temperature, are moderated by operating over a large temperature range from 0 to 300sp° C. A variable-volume view cell, capable of operating to high temperatures and high pressures, was designed and implemented to meet these extreme operating conditions. Increasing the polarizability of nonpolar solvents reduces the pressures required to dissolve FEPsb{19} by as much as 1,500 bar going from perfluoromethane to perfluoropropane. However, in polar solvents, the pressures required for FEPsb{19} solubility rise dramatically as the temperature is decreased due to the increase in polar, solvent-solvent interactions that do not favor the solubility of a nonpolar copolymer. Replacing semi-crystalline FEPsb{19} with amorphous FEPsb{48} yields the same trends in phase behavior. Therefore, crystallinity does not control the shape of these fluorocopolymer-SCF cloud-point curves. Adding a cosolvent to the solution can dramatically lower the pressures needed to dissolve the copolymer. Introducing the "cosolvent" directly into the polymer backbone by changing copolymer architecture is another method of modifying fluorocopolymer solubility as seen with the results for Fluorel-SCF mixtures compared to those for FEPsb{19}-SCF mixtures. A supercritical fractionation of FEPsb{19} provides information on the impact of molecular weight and end-group content on fluorocopolymer solubility. Challenges remain for modeling fluorocopolymer-solvent mixtures. The Sanchez-Lacombe equation cannot capture the characteristics of FEPsb{19}-SCF solvent phase behavior unless two empirical mixture parameters, one of which varies with temperature, are used.

Mertdogan, Cynthia Asli

416

Organocatalytic asymmetric assembly reactions for the syntheses of carbohydrate derivatives by intermolecular Michael-Henry reactions  

PubMed Central

Given the significance of carbohydrates in life, medicine, and industry, the development of simple and efficient de novo methods to synthesize carbohydrates are highly desirable. Organocatalytic asymmetric assembly reactio