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1

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

NASA Astrophysics Data System (ADS)

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.

2014-05-01

2

Vortices in fermion droplets with repulsive dipole-dipole interactions  

NASA Astrophysics Data System (ADS)

Vortices are found in a fermion system with repulsive dipole-dipole interactions, trapped by a rotating quasi-two-dimensional harmonic oscillator potential. Such systems have much in common with electrons in quantum dots, where rotation is induced via an external magnetic field. In contrast to the Coulomb interactions between electrons, the (externally tunable) anisotropy of the dipole-dipole interaction breaks the rotational symmetry of the Hamiltonian. This may cause the otherwise rotationally symmetric exact wave function to reveal its internal structure more directly.

Eriksson, G.; Cremon, J. C.; Manninen, M.; Reimann, S. M.

2012-10-01

3

Observation of Stueckelberg oscillations in dipole-dipole interactions  

SciTech Connect

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

Ditzhuijzen, C. S. E. van; Tauschinsky, Atreju; Van Linden van den Heuvell, H. B. [Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands)

2009-12-15

4

Dipole-dipole interactions in solution mixtures probed by two-dimensional synchronous spectroscopy based on orthogonal sample design scheme.  

PubMed

Two-dimensional (2D) synchronous spectroscopy together with a new approach called "Orthogonal Sample Design Scheme" was used to study the dipole-dipole interactions in two representative ternary chemical systems (N,N-dimethyllformamide (DMF)/CH3COOC2H5/CCl4 and C60/CH3COOC2H5/CCl4). For the first system, dipole-dipole interactions among carbonyl groups from DMF and CH3COOC2H5 are characterized by using the cross peak in 2D Fourier Transform Infrared Radiation (FT-IR) spectroscopy. For the second system, intermolecular interaction among ?-? transition from C60 and vibration transition from the carbonyl band of ethyl acetate is probed by using 2D spectra. The experimental results demonstrate that "Orthogonal Sample Design Scheme" can effectively remove interfering part that is not relevant to intermolecular interaction. Additional procedures are carried out to preclude the possibilities of producing interfering cross peaks by other reasons, such as experimental errors. Dipole-dipole interactions that manifest in the form of deviation from the Beer-Lambert law generate distinct cross peaks visualized in the resultant 2D synchronous spectra of the two chemical systems. This work demonstrates that 2D synchronous spectra coupled with orthogonal sample design scheme provide us an applicable experimental approach to probing and characterizing dipole-dipole interactions in complex molecular systems. PMID:24582337

Li, Hui-zhen; Tao, Dong-liang; Qi, Jian; Wu, Jin-guang; Xu, Yi-zhuang; Noda, Isao

2014-04-24

5

Effective dipole-dipole interactions in critical nanofluids.  

PubMed

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. PMID:23416706

Rudavets, M G

2013-05-01

6

Inclusion of magnetic dipole–dipole and hydrodynamic interactions in implant-assisted magnetic drug targeting  

Microsoft Academic Search

Mathematical modelling of the implant-assisted magnetic drug targeting system of Avilés, Ebner and Ritter is performed. In order to model the agglomeration of particles known to occur in this system, the magnetic dipole–dipole and hydrodynamic interactions are included. Such interactions were calculated previously by Mikkelsen et al. under low magnetic fields (~0.05T) in microfluidic systems. Here, a higher magnetic field

P. J. Cregg; Kieran Murphy; Adil Mardinoglu

2009-01-01

7

Population Dynamics in Cold Gases Resulting from the Long-Range Dipole-Dipole Interaction  

E-print Network

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

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

2009-06-24

8

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

NASA Astrophysics Data System (ADS)

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

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

2012-03-01

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

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

11

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

PubMed

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. PMID:25001313

Yu, Yue; Luo, Zhuxi; Wang, Ziqiang

2014-07-30

12

Spatially Resolved Observation of Dipole-Dipole Interaction between Rydberg Atoms  

SciTech Connect

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

Ditzhuijzen, C. S. E. van; Noordam, L. D.; Heuvell, H. B. van Linden van den [Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands); Koenderink, A. F. [FOM-Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam (Netherlands); Hernandez, J. V.; Robicheaux, F. [Department of Physics, Auburn University, Alabama 36849-5311 (United States)

2008-06-20

13

Entangling Dipole-Dipole Interactions and Quantum Logic in Optical Lattices  

E-print Network

We study a means of creating multiparticle entanglement of neutral atoms using pairwise controlled dipole-dipole interactions in a three dimensional optical lattice. For tightly trapped atoms the dipolar interaction energy can be much larger than the photon scattering rate, and substantial coherent evolution of the two-atom state can be achieved before decoherence occurs. Excitation of the dipoles can be made conditional on the atomic states, allowing for deterministic generation of entanglement. We derive selection rules and a figure-of-merit for the dipole-dipole interaction matrix elements, for alkali atoms with hyperfine structure and trapped in well localized center of mass states. Different protocols are presented for implementing two-qubits quantum logic gates such as the controlled-phase and swap gate. We analyze the fidelity of our gate designs, imperfect due to decoherence from cooperative spontaneous emission and coherent couplings outside the logical basis. Outlines for extending our model to include the full molecular interactions potentials are discussed.

G. K. Brennen; I. H. Deutsch; P. S. Jessen

1999-10-07

14

Inclusion of magnetic dipole-dipole and hydrodynamic interactions in implant-assisted magnetic drug targeting  

NASA Astrophysics Data System (ADS)

Mathematical modelling of the implant-assisted magnetic drug targeting system of Avilés, Ebner and Ritter is performed. In order to model the agglomeration of particles known to occur in this system, the magnetic dipole-dipole and hydrodynamic interactions are included. Such interactions were calculated previously by Mikkelsen et al. under low magnetic fields (~0.05 T) in microfluidic systems. Here, a higher magnetic field (0.7 T) is considered and the effect of interactions on two nanoparticles with a seed implant is calculated. The calculations were performed with the open-source software OpenFOAM. Different initial positions are considered and the system performance is assessed in terms of capture cross section. Inclusion of both interactions was seen to alter the capture cross section of the system by up to 7% in absolute terms.

Cregg, P. J.; Murphy, Kieran; Mardinoglu, Adil

2009-12-01

15

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

16

Contribution of dipole-dipole interactions to the stability of the collagen triple helix  

PubMed Central

Unveiling sequence–stability and structure–stability relationships is a major goal of protein chemistry and structural biology. Despite the enormous efforts devoted, answers to these issues remain elusive. In principle, collagen represents an ideal system for such investigations due to its simplified sequence and regular structure. However, the definition of the molecular basis of collagen triple helix stability has hitherto proved to be a difficult task. Particularly puzzling is the decoding of the mechanism of triple helix stabilization/destabilization induced by imino acids. Although the propensity-based model, which correlates the propensities of the individual imino acids with the structural requirements of the triple helix, is able to explicate most of the experimental data, it is unable to predict the rather high stability of peptides embedding Gly–Hyp–Hyp triplets. Starting from the available X-ray structures of this polypeptide, we carried out an extensive quantum chemistry analysis of the mutual interactions established by hydroxyproline residues located at the X and Y positions of the Gly–X–Y motif. Our data clearly indicate that the opposing rings of these residues establish significant van der Waals and dipole–dipole interactions that play an important role in triple helix stabilization. These findings suggest that triple helix stabilization can be achieved by distinct structural mechanisms. The interplay of these subtle but recurrent effects dictates the overall stability of this widespread structural motif. PMID:18369197

Improta, Roberto; Berisio, Rita; Vitagliano, Luigi

2008-01-01

17

Interstrand Dipole-Dipole Interactions Can Stabilize the Collagen Triple Helix*  

PubMed Central

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

Shoulders, Matthew D.; Raines, Ronald T.

2011-01-01

18

Radio-frequency-driven dipole-dipole interactions in spatially separated volumes  

NASA Astrophysics Data System (ADS)

Radio-frequency (rf) fields in the MHz range are used to induce resonant energy transfer between cold Rydberg atoms in spatially separated volumes. After laser preparation of the Rydberg atoms, dipole-dipole coupling excites the 49s atoms in one cylinder to the 49p state while the 41d atoms in the second cylinder are transferred down to the 42p state. The energy exchanged between the atoms in this process is 33GHz . An external rf field brings this energy transfer into resonance. The strength of the interaction has been investigated as a function of amplitude (0-1V/cm) and frequency (1-30MHz) of the rf field and as a function of a static-field offset. Multiphoton transitions up to fifth order as well as selection rules prohibiting the process at certain fields have been observed. The width of the resonances has been reduced compared to earlier results by switching off external magnetic fields of the magneto-optical trap, making sub-MHz spectroscopy possible. All features are well reproduced by theoretical calculations taking the strong ac Stark shift due to the rf field into account.

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

2008-12-01

19

Effects of Dipole-Dipole Interaction on the Transmitted spectrum of Two-level Atoms trapped in an optical cavity  

E-print Network

The transmission spectrum of two dipole-dipole coupled atoms interacting with a single-mode optical cavity in strong coupling regime is investigated theoretically for the lower and higher excitation cases, respectively. The dressed states containing the dipole-dipole interaction (DDI) are obtained by transforming the two-atom system into an effective single-atom one. We found that the DDI can enhance the effects resulting from the positive atom-cavity detunings but weaken them for the negative detunings cases for lower excitation, which can promote the spectrum exhibiting two asymmetric peaks and shift the heights and the positions of them. For the higher excitation cases, DDI can augment the atomic saturation and lead to the deforming of the spectrum. Furthermore, the large DDI can make the atom and the cavity decouple, making a singlet of the normal-mode spectrum.

Yuqing Zhang; Lei Tan; Peter Barker

2012-07-12

20

Analysis of a quantum logic device based on dipole-dipole interactions of optically trapped Rydberg atoms  

SciTech Connect

We present a detailed analysis and design of a neutral atom quantum logic device based on atoms in optical traps interacting via dipole-dipole coupling of Rydberg states. The dominant physical mechanisms leading to decoherence and loss of fidelity are enumerated. Our results support the feasibility of performing single- and two-qubit gates at MHz rates with decoherence probability and fidelity errors at the level of 10{sup -3} for each operation. Current limitations and possible approaches to further improvement of the device are discussed.

Saffman, M.; Walker, T.G. [Department of Physics, University of Wisconsin, 1150 University Avenue, Madison, Wisconsin 53706 (United States)

2005-08-15

21

Analysis of a quantum logic device based on dipole-dipole interactions of optically trapped Rydberg atoms  

E-print Network

We present a detailed analysis and design of a neutral atom quantum logic device based on atoms in optical traps interacting via dipole-dipole coupling of Rydberg states. The dominant physical mechanisms leading to decoherence and loss of fidelity are enumerated. Our results support the feasibility of performing single and two-qubit gates at MHz rates with decoherence probability and fidelity errors at the level of $10^{-3}$ for each operation. Current limitations and possible approaches to further improvement of the device are discussed.

M. Saffman; T. G. Walker

2005-02-09

22

Cross Correlation between the Dipole-Dipole Interaction and the Curie Spin Relaxation: The Effect of Anisotropic Magnetic Susceptibility  

NASA Astrophysics Data System (ADS)

Cross-correlated relaxation caused by the interference of nuclear dipole-dipole interaction and the Curie spin relaxation (DD-CSR cross relaxation) is generalized to treat the case of anisotropic magnetic susceptibility, including the important case where the latter originates from zero-field splitting. It is shown that the phenomenon of DD-CSR cross relaxation is absolutely general and to be expected under any electronic configuration. The results of the generalization are presented for a model system, and the consequences for paramagnetic metalloproteins are illustrated with an example of cerium(III)-substituted calbindin. The effects of the magnetic anisotropy are found to be substantial.

Bertini, Ivano; Kowalewski, Jozef; Luchinat, Claudio; Parigi, Giacomo

2001-09-01

23

Observation of Suppression of Light Scattering Induced by Dipole-Dipole Interactions in a Cold-Atom Ensemble  

NASA Astrophysics Data System (ADS)

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 number of atoms from 1 to ˜450, we observe a broadening of the line, a small redshift and, consistently with these, a strong suppression of the scattered light with respect to the noninteracting atom case. We compare our data to numerical simulations of the optical response, which include the internal level structure of the atoms.

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

2014-09-01

24

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

PubMed

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 number of atoms from 1 to ?450, we observe a broadening of the line, a small redshift and, consistently with these, a strong suppression of the scattered light with respect to the noninteracting atom case. We compare our data to numerical simulations of the optical response, which include the internal level structure of the atoms. PMID:25302887

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

2014-09-26

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

Effects of dipole-dipole interaction on the transmitted spectrum of two-level atoms trapped in an optical cavity  

NASA Astrophysics Data System (ADS)

The transmission spectrum of two dipole-coupled atoms interacting with a single-mode optical cavity in the strong coupling regime is investigated theoretically for the lower and higher excitation cases. The dressed states containing the dipole-dipole interaction (DDI) are obtained by transforming the two-atom system into an effective single-atom system. We find that the DDI can enhance the effects resulting from the positive atom-cavity detunings but weakens them for the negative detuning cases for the lower excitation, which causes the spectrum to exhibit two asymmetric peaks with shifted heights and positions. For the higher excitation cases, the DDI augments the atomic saturation and leads to the deforming of the spectrum. Furthermore, the large DDI can cause the atom and the cavity to decouple, producing a singlet of the normal-mode spectrum.

Zhang, Yu-Qing; Tan, Lei; Barker, Peter

2014-04-01

27

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

SciTech Connect

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

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

1994-12-01

28

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

SciTech Connect

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

Berezovsky, V. V. [Lomonosov Pomor State University (Russian Federation); Men'shikov, L. I. [Russian Research Centre Kurchatov Institute (Russian Federation); Oberg, S.; Latham, C. D. [Lulea University of Technology (Sweden)

2008-07-15

29

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

30

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

31

Determination of Nanocrystal Size Distribution in Magnetic Multicore Particles Including Dipole-Dipole Interactions and Magnetic Anisotropy: a Monte Carlo Study  

NASA Astrophysics Data System (ADS)

A correct estimate of the size distribution (i.e., median diameter D and geometric standard deviation ?) of the magnetic nanocrystals (MNCs) embedded in magnetic multicore particles is a necessity in most applications relying on the magnetic response of these particles. In this paper we use a Monte Carlo method to simulate the equilibrium magnetization of two types of multicore particles: (I) MNCs fused in a random compact cluster, and (II) MNCs distributed on the surface of a large carrier sphere. The simulated magnetization data are then fitted using a common method based on a Langevin equation weighted with a size distribution function. Finally, the fitting parameters Dm and ?m are compared to the real parameters Dp and ?p used to generate the MNCs. Our results show that fitting magnetization data with a Langevin model that neglects magnetic anisotropy and dipole-dipole interactions leads to an erroneous estimate of the size distribution of the MNCs in multicore particles. The magnitude of the error depends on the particle morphology, number of MNCs contained in the particle and magnetic properties of the MNCs.

Schaller, Vincent; Wahnström, Göran; Sanz-Velasco, Anke; Enoksson, Peter; Johansson, Christer

2010-12-01

32

Magnetic sponge phenomena associated with interchain dipole-dipole interactions in a series of ferrimagnetic chain compounds doped with minor diamagnetic species.  

PubMed

The donor/acceptor ionic chain (i.e., the D(+)A(-) chain) [Ru2(2-MeO-4-ClPhCO2)4(BTDA-TCNQ)]·2.5(benzene) (1; 2-MeO-4-ClPhCO2(-) = 2-methoxy-4-chlorobenzoate; BTDA-TCNQ = bis(1,2,5-thiadiazolo)tetracyanoquinodimethane) is a ferrimagnetic chain with S = 3/2 from [Ru2(II,III)](+) (i.e., D(+)) and S = 1/2 from BTDA-TCNQ(•-) (i.e., A(-)), with J ? -100 K, in which long-range antiferromagnetic ordering at TN = 11 K occurs because interchain antiferromagnetic interactions are critical. Compound 1 undergoes a reversible crystal-to-crystal structural transformation with the elimination/absorption of the crystallization solvent to form the dried compound [Ru2(2-MeO-4-ClPhCO2)4(BTDA-TCNQ)] (1'), which has a higher TN (14 K). This change is clearly caused by the shortening of the interchain distances because the exchange coupling parameter for the chain is the same in both 1 and 1'. The chain compounds in 1 can be doped with minor diamagnetic [Rh2(II,II)] species, [{(Ru2)(1-x)(Rh2)(x)(2-MeO-4-ClPhCO2)4}(BTDA-TCNQ)]·2.5(benzene) (x = 0.03 for Rh-3%; x = 0.05 for Rh-5%; x = 0.16 for Rh-16%), which shifts the TN to lower temperatures, the magnitude of the shift being dependent on the doping ratio x (TN = 5.9 K for Rh-3%, TN = 3.7 K for Rh-5%, and TN was not observed above 1.8 K for Rh-16%). Drying a doped compound increased its TN, as was found for 1': TN = 9.9 K for Rh-3%', TN = 9.2 K for Rh-5%', and TN was not observed above 1.8 K for Rh-16%'. TN had a linear relationship with the doping ratio x of the [Rh2] species in both the fresh and dried compounds. The TN linear relationship is associated with the magnitude of the effective magnetic dipole (i.e., the average correlation length) in the chains caused by the [Rh2] defects as well as naturally generated defects in the synthetic process and with the interchain distances affected by the crystal-to-crystal transformations. These results demonstrate that slightly modifying the short-range correlation lengths, which changes the magnetic dipole magnitudes, strongly affects the bulk antiferromagnetic transition, with key dipole-dipole interactions, in low-dimensional anisotropic systems. PMID:24750071

Nishio, Masaki; Miyasaka, Hitoshi

2014-05-01

33

Energy Driven Pattern Formation in Planar Dipole-Dipole Systems in the Presence of Weak Noise  

E-print Network

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

Jaron Kent-Dobias; Andrew J. Bernoff

2014-06-14

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

Helping Students Assess the Relative Importance of Different Intermolecular Interactions  

ERIC Educational Resources Information Center

A semi-quantitative model has been developed to estimate the relative effects of dispersion, dipole-dipole interactions, and H-bonding on the normal boiling points ("T[subscript b]") for a subset of simple organic systems. The model is based upon a statistical analysis using multiple linear regression on a series of straight-chain organic…

Jasien, Paul G.

2008-01-01

36

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

USGS Publications Warehouse

An interactive HP 9845B BASIC program transforms continuous polar dipole-dipole resistivity soundings to half-Schlumberger soundings. The program features graphic presentation of the field dipole-dipole data as well as the transformed half-Schlumberger data. An example of the transformation and its effectiveness in smoothing "high-frequency" noise is given. ?? 1990.

Zerilli, A.; Bisdorf, R.J.

1990-01-01

37

Intermolecular Attractions  

NSDL National Science Digital Library

Intermolecular attractions are responsible for everything from the temperatures at which substances boil to the power of your immune system in recognizing pathogens and the climbing ability of geckos! Feel the strength of London dispersion and dipole-dipole attractions, explore how intermolecular attractions affect boiling point and solubility, and investigate the special role of hydrogen bonds in DNA. Finally, design your own antibody based on intermolecular attractions.

Consortium, The C.

2011-12-11

38

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

39

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

SciTech Connect

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

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

2006-01-07

40

Computational studies on intermolecular interactions in solvation  

NASA Astrophysics Data System (ADS)

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

Song, Weiping

41

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

42

Interactions in dendronized polymers: intramolecular dominates intermolecular.  

PubMed

In an attempt to relate atomistic information to the rheological response of a large dendritic object, interand intramolecular hydrogen bonds and p,p-interactions have been characterized in a dendronized polymer (DP) that consists of a polymethylmethacrylate backbone with tree-like branches of generation four (PG4) and contains both amide and aromatic groups. Extensive atomistic molecular dynamics simulations have been carried out on (i) an isolated PG4 chain and (ii) ten dimers formed by two PG4 chains associated with different degrees of interpenetration. Results indicate that the amount of nitrogen atoms involved in hydrogen bonding is ~11% while ~15% of aromatic groups participate in p,pinteractions. Furthermore, in both cases intramolecular interactions clearly dominate over intermolecular ones, while exhibiting markedly different behaviors. Specifically, the amount of intramolecular hydrogen bonds increases when the interpenetration of the two chains decreases, whereas intramolecular p,pinteractions remain practically insensitive to the amount of interpenetration. In contrast, the strength of the corresponding two types of intermolecular interactions decreases with interpenetration. Although the influence of complexation on the density and cross-sectional radius is relatively small, interpenetration affects significantly the molecular length of the DP. These results support the idea of treating DPs as long colloidal molecules. PMID:24983117

Córdova-Mateo, Esther; Bertran, Oscar; Zhang, Baozhong; Vlassopoulos, Dimitris; Pasquino, Rossana; Schlüter, A Dieter; Kröger, Martin; Alemán, Carlos

2014-02-21

43

Intermolecular interactions in a radiation field via the method of induced moments  

SciTech Connect

Molecular quantum electrodynamics is employed to calculate a generalized formula for the energy shift between a pair of molecules that have electric polarizability of arbitrary multipole order and are in the presence of an intense electromagnetic field. In contrast to a previous calculation of the dipole-dipole contribution, which required fourth-order time-dependent perturbation theory for its evaluation, the present approach involves calculating the interaction between the multipole moments induced at each center by the incident beam and the resonant multipole-multipole coupling tensor together with the average value of the spatial correlation function of the displacement field for an N-photon state. The theory developed applies to the situation where the molecular pair is held fixed relative to the direction of propagation of the radiation field or is allowed to be completely randomly oriented. Explicit results are obtained for dipole-quadrupole and quadrupole-quadrupole polarizable molecules. For oriented systems the energy shift for linear and circular polarizations is examined for incident radiation propagating in directions parallel and perpendicular to the intermolecular join, and the asymptotic behavior is obtained at the limits of short and large separation distance. After performing a pair orientation average, the energy shift in the near zone is found to exhibit an R{sup -1} power-law behavior with separation distance, while the far zone has a modulated R{sup -2} dependence in all of the cases considered. None of the energy shifts obtained display discriminatory characteristics, with respect to either the handedness of the incident beam or the individual species.

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

2006-01-15

44

Intermolecular interactions in lipid/carotenoid monolayers.  

PubMed Central

The collapse pressure at the air-water interface of monomolecular films of 1,2-distearoyl derivatives of phosphatidylcholine and digalactosyldiacylglycerol containing various proportions of the carotenoid astaxanthin was related to the composition of the monolayer. The results were analysed by using a regular-association approximation by which it is assumed that there is a stepwise formation of ABi-type associations where A and B represent the diacyl lipid and astaxanthin respectively and 1 less than or equal to i less than or equal to 6. This treatment provides an adequate description of the experimental data and permits calculation of equilibrium constants for the steps in complex-formation; each step is said to have the same equilibrium constant. The value for the collapse-surface-pressure increment associated with formation of ABi complexes was also derived. Calculated values of equilibrium constants and collapse-surface-pressure increments are greater for phosphatidylcholine/astaxanthin mixed monolayers than for digalactosyldiacylglycerol/astaxanthin mixed monolayers. These differences are discussed in terms of intermolecular interactions between components in the two systems. PMID:3435489

Tomoaia-Cotisel, M; Zsako, J; Chifu, E; Quinn, P J

1987-01-01

45

Weak Intermolecular Interactions in an Ionically Bound Molecular Adsorbate: Cyclopentadienyl/Cu(111)  

NASA Astrophysics Data System (ADS)

The dissociative adsorption of cyclopentadiene (C5H6) on Cu(111) yields a cyclopentadienyl (Cp) species with strongly anionic characteristics. The Cp potential energy surface and frictional coupling to the substrate are determined from measurements of dynamics of the molecule together with density functional calculations. The molecule is shown to occupy degenerate threefold adsorption sites and molecular motion is characterized by a low diffusional energy barrier of 40±3meV with strong frictional dissipation. Repulsive dipole-dipole interactions are not detected despite charge transfer from substrate to adsorbate.

Hedgeland, H.; Lechner, B. A. J.; Tuddenham, F. E.; Jardine, A. P.; Allison, W.; Ellis, J.; Sacchi, M.; Jenkins, S. J.; Hinch, B. J.

2011-05-01

46

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

47

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

NASA Astrophysics Data System (ADS)

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

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

1998-07-01

48

Direct observation of intermolecular interactions mediated by hydrogen bonding.  

PubMed

Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N-H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to correlated nuclear motions and significant changes in the vibrational structure of the amide group. These observations have direct impact on modeling and interpreting the IR spectra of proteins. In addition, they illustrate a general approach to direct molecular characterization of intermolecular interactions. PMID:25053321

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

2014-07-21

49

Quantum discord in spin systems with dipole-dipole interaction  

NASA Astrophysics Data System (ADS)

The behavior of total quantum correlations (discord) in dimers consisting of dipolar-coupled spins 1/2 are studied. We found that the discord at absolute zero temperature. As the temperature increases, the quantum correlations in the system increase at first from zero to its maximum and then decrease to zero according to the asymptotic law . It is also shown that in absence of external magnetic field , the classical correlations at are, vice versa, maximal. Our calculations predict that in crystalline gypsum the value of natural quantum discord between nuclear spins of hydrogen atoms is maximal at the temperature of 0.644 K, and for 1,2-dichloroethane ClC- the discord achieves the largest value at K. In both cases, the discord equals bit/dimer what is of its upper limit in two-qubit systems. We estimate also that for gypsum at room temperature bit/dimer, and for 1,2-dichloroethane at K the discord is bit per a dimer.

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

2013-11-01

50

Weak intermolecular interactions between nitrogen and oxygen atoms  

NASA Astrophysics Data System (ADS)

A recent study of organic crystalline compounds containing nitro groups, which concentrated on the intermolecular approach of oxygen to the N of the NO 2 group, has revealed typical N…O distances much shorter than would be expected from the van der Waals radii. Ab initio dimer calculations reported here substantiate this finding, and indicate that these interactions are comparable in strength with weak hydrogen bonds. Dimer binding energies of 10-13 kJ mol -1 are obtained at the MP2/6-31++G ?? level, and the optimal N…O distance is ? 2.85 Å. The difference between one-electron (Hartree-Fock) and correlated treatments, combined with an atoms-in-molecules decomposition of the charge distribution, suggests that this interaction is dominated by dispersive forces.

Platts, J. A.; Howard, S. T.; Wo?niak, K.

1995-01-01

51

Intermolecular Interactions in Biomolecular Systems Examined by Mass Spectrometry  

NASA Astrophysics Data System (ADS)

With the development of electrospray and matrix-assisted laser desorption ionization, mass spectrometry (MS) evolved into a powerful tool in the field of biochemistry. Whereas MS is primarily analytical in nature, an increasing number of MS research groups employ the method to address fundamental biochemical questions. Probing the interaction of noncovalently bound molecules in the mass spectrometer is one of the most interesting MS-based experiments possible today, with the potential of making a significant contribution to the basic understanding of the structure and function of biochemical complexes. Here we review a number of current research efforts employing primarily MS techniques to investigate intermolecular interactions in biochemical systems. Examples chosen include the interaction of biomolecules with solvent molecules; interactions between nucleic-acid molecules, in particular, interactions in duplex and quadruplex structures; and interactions between proteins involved in neurodegenerative diseases. Finally we conclude by presenting a few examples of very large biomolecular assemblies in the mega-Dalton range analyzed by MS.

Wyttenbach, Thomas; Bowers, Michael T.

2007-05-01

52

Role of Intermolecular Interactions of Vesicular Stomatitis Virus Nucleoprotein in RNA Encapsidation  

Microsoft Academic Search

The crystal structure of the vesicular stomatitis virus nucleoprotein (N) in complex with RNA reveals extensive and specific intermolecular interactions among the N molecules in the 10-member oligomer. What roles these interactions play in encapsidating RNA was studied by mutagenesis of the N protein. Three N mutants intended for disruption of the intermolecular interactions were designed and coexpressed with the

Xin Zhang; Todd J. Green; Jun Tsao; Shihong Qiu; Ming Luo

2008-01-01

53

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

54

Localized-overlap approach to calculations of intermolecular interactions  

NASA Astrophysics Data System (ADS)

Symmetry-adapted perturbation theory (SAPT) based on the density functional theory (DFT) description of the monomers [SAPT(DFT)] is one of the most robust tools for computing intermolecular interaction energies. Currently, one can use the SAPT(DFT) method to calculate interaction energies of dimers consisting of about a hundred atoms. To remove the methodological and technical limits and extend the size of the systems that can be calculated with the method, a novel approach has been proposed that redefines the electron densities and polarizabilities in a localized way. In the new method, accurate but computationally expensive quantum-chemical calculations are only applied for the regions where it is necessary and for other regions, where overlap effects of the wave functions are negligible, inexpensive asymptotic techniques are used. Unlike other hybrid methods, this new approach is mathematically rigorous. The main benefit of this method is that with the increasing size of the system the calculation scales linearly and, therefore, this approach will be denoted as local-overlap SAPT(DFT) or LSAPT(DFT). As a byproduct of developing LSAPT(DFT), some important problems concerning distributed molecular response, in particular, the unphysical charge-flow terms were eliminated. Additionally, to illustrate the capabilities of SAPT(DFT), a potential energy function has been developed for an energetic molecular crystal of 1,1-diamino-2,2-dinitroethylene (FOX-7), where an excellent agreement with the experimental data has been found.

Rob, Fazle

55

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

NASA Astrophysics Data System (ADS)

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

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

2008-10-01

56

Determination of structural characteristics of all-organic radical liquid crystals based on analysis of the dipole-dipole broadened EPR spectra.  

PubMed

The angular dependences of g-value and line width of EPR spectra of paramagnetic all-organic liquid crystalline (LC) materials were measured for the quantitative characterization of the nematic, cholesteric, and smectic C phases. The detailed molecular alignment in mesophases was determined by means of numerical spectra simulation focusing on spin exchange and dipole-dipole magnetic interactions of neighboring molecules. The obtained structural data indicate that the spin polarization mechanism between neighboring molecules rather than the direct through-space interactions between paramagnetic centers is responsible for the specific magnetic properties of the studied LC materials. PMID:24479531

Vorobiev, A Kh; Chumakova, N A; Pomogailo, D A; Uchida, Y; Suzuki, K; Noda, Y; Tamura, R

2014-02-20

57

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

58

Electronic Structure Theory for Radicaloid Systems and Intermolecular Interactions  

NASA Astrophysics Data System (ADS)

A radical molecule contains one or more electrons that are unpaired. A radicaloid may be defined as a molecule in which there are that are partially unpaired. As a result, the electronic structure of the radicaloid can be quite complicated for a variety of reasons. For a singlet biradicaloid, the singlet and triplet wavefunction can be quite close energetically which can lead to problems when trying to describe the system with a single determinant. The simplest solution to this problem is to allow the wavefunction to break spin-symmetry in order to get a lower energy. Unfortunately this action can lead to wavefunctions that are no longer eigenfunctions of the < S2> operator. In the second chapter we investigate a distannyne which has a biradicaloid resonance structure. By examining the orbital Hessian, it is discovered that the spin-symmetric solution is a saddle-point in wavefunction space and is structurally different than the spin-polarized solution. We then increase the complexity of the model system and see that the spin-symmetric solution is only a minimum for the exact experimental system and not for a simplified model system in which bulky organic substituents are replaced by simpler phenyl groups. Therefore, the breaking of spin-symmetry is absolutely critical in the small model systems and the full substituents play a non-trivial role. However, the breaking of the spin-symmetry can have consequences for physical quantities when correlated methods are used. At the point of spin polarization or unrestriction the orbital Hessian will have one eigenvalue which is zero. Since the relaxed density matrix in correlated methods like Second-Order Mo ller-Plesset theory (MP2) depend on the inverse of the Hessian, at the unrestriction point this quantity will be undefined. Some unphysical artifacts are identified as a direct consequence of this fact. First, discontinuities in first order molecular properties such as the dipole moment are seen at the geometries associated with unrestriction. Second, the relaxed density matrix itself fails to be N-representable, with natural orbital occupation numbers less than zero and greater than one. Therefore, it is desirable to use a method that is not dependent on the inverse of the Hessian like orbital optimized MP2 (O2). Another system which requires the use of orbital optimization is a neutral soliton on a polyacetylene chain. In this system, the Hartree-Fock reference suffers from severe spin-polarization making the wavefunction physically unreasonable unless a very sophisticated treatment of electron correlation is used to correct this problem. Originally, it was found that computationally expensive methods like CCSD(T) and CASSCF could adequately describe small model chain but not the full system. The O2 method is found to be an dramatic improvement over traditional MP2 which can be feasibly applied to polyenyl chains long enough to characterize the soliton. It is also discovered that density functionals are generally inadequate in describing the half-width of the soliton. Finally, the last chapter takes a slightly different perspective and focuses on the addition of correlation energy to a successful energy decomposition analysis based on absolutely localized molecular orbitals. It is discovered that the resulting new method can adequately describe systems with dispersive intermolecular interactions and large amounts of charge transfer. This scheme is then applied to the water dimer systems and it is found that all of the intermolecular interactions similar in size with the electrostatic interaction being the largest and the dispersive interaction being the smallest. This method is also contrasted with other EDA schemes.

Kurlancheek, Westin

59

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

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

60

Comparison of Wenner and dipole-dipole arrays in the study of an underground three-dimensional cavity  

NASA Astrophysics Data System (ADS)

The objective of this paper was to compare Wenner and dipole-dipole configurations in delineating an underground cavity at a site near the University of Malaya, Malaysia. A three-dimensional electrical resistivity imaging survey was carried out along seven parallel lines using Wenner and dipole-dipole arrays. A three-dimensional least-squares algorithm, based on the robust inversion method, was used in the inversion of the apparent resistivity data. In the inverted model, both the horizontal and vertical extents of the anomalous zones were displayed. Results indicate the superiority of the Wenner array over the dipole-dipole array for determining the vertical distribution of the subsurface resistivity, although the dipole-dipole array produced a better lateral extent of the subsurface features. The results show that the three-dimensional electrical resistivity imaging survey using both the Wenner and dipole-dipole arrays, in combination with an appropriate three-dimensional inversion method and synthetic model analysis, can be highly useful for engineering and environmental applications, especially for underground three-dimensional cavity detection.

Neyamadpour, Ahmad; Abdullah, W. A. T. Wan; Taib, Samsudin; Neyamadpour, Behrang

2010-03-01

61

Rational targeting of subclasses of intermolecular interactions: elimination of nonspecific binding for analyte sensing.  

PubMed

The ability to target and control intermolecular interactions is crucial in the development of several different technologies. Here we offer a tool to rationally design liquid media systems that can modulate specific intermolecular interactions. This has broad implications in deciphering the nature of intermolecular forces in complex solutions and offers insight into the forces that govern both specific and nonspecific binding in a given system. Nonspecific binding still continues to be a problem when dealing with analyte detection across a range of different detection technologies. Here, we exemplify the problem of nonspecific binding on model membrane systems and when dealing with low-abundance protein detection on commercially available SPR technology. A range of different soluble reagents that target specific subclasses of intermolecular interactions have been tested and optimized to virtually eliminate nonspecific binding while leaving specific interactions unperturbed. Thiocyanate ions are used to target nonpolar interactions, and small reagents such as glycylglycylglycine are used to modulate the dielectric constant, which targets charge-charge and dipole interactions. We show that with rational design and careful modulation these reagents offer a step forward in dissecting the intermolecular forces that govern binding, alongside offering nonspecific binding elimination in detection systems. PMID:25046104

Lane, Jordan S; Richens, Joanna L; Vere, Kelly-Ann; O'Shea, Paul

2014-08-12

62

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

2014-10-21

63

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

64

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

SciTech Connect

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

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

2012-04-28

65

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

PubMed

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

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

2014-10-23

66

Intermolecular interactions of the malate synthase of Paracoccidioides spp  

PubMed Central

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

2013-01-01

67

Isomerization and intermolecular solutesolvent interactions of ethyl isocyanate: Ultrafast infrared vibrational echoes and linear  

E-print Network

. At very low temperature, below the 2MP glass transition, isomerization cannot occur. The absorption spectra show complex behavior as a function of temperature from room temperature to 8 K. The EIC data and intermolecular dynamical interactions. At room temperature, gauche­trans isomerization is very fast

Fayer, Michael D.

68

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

69

Approximate exchange perturbation study of intermolecular interactions in molecular complexes  

Microsoft Academic Search

In an attempt to rationalize and improve an approximate exchange perturbation scheme related to the model of Murrell et al., more accurate approximations are introduced eliminating the use of empirical parameters. The total interaction energy was evaluated as the sum of additive electrostatic, exchange, charge transfer, and dispersion contributions. It is proven that the assumption of intramolecular ZDO approximation is

W. Andrzej Sokalski; Henryk Chojnacki

1978-01-01

70

Interplay between molecular conformation and intermolecular interactions in conformational polymorphism: a molecular perspective from electronic calculations of tolfenamic acid.  

PubMed

Tolfenamic acid exhibits conformational polymorphism. The molecules in its two commonly occurred crystal structures form similar hydrogen-bonded dimers but differ in conformation. The conformational variance was analyzed by electronic calculation methods with the aim to unravel intrinsic connection between the conformational flexibility and intermolecular interactions in the polymorphs. The study was conducted mainly by conceptual density functional theory (DFT) and natural bond orbital (NBO) analysis. It is found that the conformational polymorphism is resulted from the energy competition between intramolecular ?-conjugation and intermolecular hydrogen bonding. By adapting conformation that departs from being the most energetically stable, tolfenamic acid molecules can strengthen the intermolecular hydrogen-bonding interactions in the crystals. The study illustrates how the molecule's electronic properties are influenced by conformational variation and, inherently, how the intermolecular interactions become regulated. Moreover, understanding molecular interaction and crystal packing necessitates electronic structure calculation and analysis, which can be further facilitated by utilizing DFT and NBO concepts. PMID:21570454

Mattei, Alessandra; Li, Tonglei

2011-10-14

71

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

PubMed

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

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

2014-11-01

72

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

73

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

Fernandez, Cristina; Minton, Allen P.

2012-01-01

74

Thz Spectroscopy and DFT Modeling of Intermolecular Vibrations in Hydrophobic Amino Acids  

NASA Astrophysics Data System (ADS)

Vibrations that involve intermolecular displacements occur in molecular crystals at frequencies in the 0.5-5 THz range (˜15-165 cm^{-1}), and these motions are direct indicators of the interaction potential between the molecules. The intermolecular potential energy surface of crystalline hydrophobic amino acids is inherently interesting simply because of the wide variety of forces (electrostatic, dipole-dipole, hydrogen-bonding, van der Waals) that are present. Furthermore, an understanding of these particular interactions is immediately relevant to important topics like protein conformation and pharmaceutical polymorphism. We measured the low-frequency absorption spectra of several polycrystalline hydrophobic amino acids using THz time-domain spectroscopy, and in addition we carried out DFT calculations using periodic boundary conditions and an exchange-correlation functional that accounts for van der Waals dispersion forces. We chose to investigate a series of similar amino acids with closely analogous unit cells (leucine, isoleucine, and allo-isoleucine, in racemic or pseudo-racemic mixtures). This allows us to consider trends in the vibrational spectra as a function of small changes in molecular arrangement and/or crystal geometry. In this way, we gain confidence that peak assignments are not based on serendipitous similarities between calculated and observed features.

Williams, michael R. C.; Aschaffenburg, Daniel J.; Schmuttenmaer, Charles A.

2013-06-01

75

[Overview of structural study on conformations and intermolecular interactions of biomolecules].  

PubMed

Information on the conformational feature and specific intermolecular interaction of biomolecules is important to understand the biological function and to develop device for treating disorder caused by the abnormal function. Thus the 3D structures of the biologically active molecules and the specific interactions with their target molecules at the atomic level have been investigated by various physicochemical approaches. Herein, the following five subjects are reviewed: (1) function-linked conformations of biomolecules including natural annular products, opioid peptides and neuropeptides; (2) ?-? stacking interactions of tryptophan derivatives with coenzymes and nucleic acid bases; (3) mRNA cap recognition of eukaryotic initiation factor 4E and its regulation by 4E-binding protein; (4) conformational feature of histamine H2 receptor antagonists and design of cathepsin B inhibitors; (5) self-aggregation mechanism of tau protein and its inhibition. PMID:22790026

Ishida, Toshimasa

2012-01-01

76

The effects of P-T changes on intermolecular interactions in crystal structure of iodoform  

NASA Astrophysics Data System (ADS)

The structural transition at different pressures of a halogen and hydrogen bonded molecular structure (iodoform, CHI3) is described. The pressures analyzed up to sample decomposition are 0.85 GPa (P1RT) and 2.15 GPa (P2RT); also room conditions (P0RT) and low temperature (106 K, P0LT) structures have been reported for comparison. The observed disorder-order phase transition, from P63/m to P63 space group, can be rationalized by the intermolecular interaction analysis. The shortening of the distances among iodoform planes, observed during the compression and the temperature decreasing, determines an ordering of molecular dipoles in a parallel arrangement: this phase transition causes a shortening of I⋯I halogen bondings. The BSSE corrected cohesive energies have been calculated for all structures at DFT/B3LYP level of theory using a periodic boundary condition code and the Grimme dispersion correction. Hirshfeld surfaces and electrostatic potential mapped on charge density isosurfaces have been computed and their features have been analyzed, in order to better understand the halogen intermolecular interactions that control the structural modification of iodoform crystal.

Bertolotti, Federica; Curetti, Nadia; Benna, Piera; Gervasio, Giuliana

2013-06-01

77

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

PubMed

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

McKenzie, S; Kang, H C

2014-12-21

78

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.

79

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

PubMed

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). PMID:25168003

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

2015-02-01

80

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

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

Intermolecular interactions in the N?C C?C H dimer  

NASA Astrophysics Data System (ADS)

Ab initio calculations on N?C-C?C-H and its anti-parallel dimer are reported, with a view to studying the intermolecular interactions present. Following initial optimisation of the monomer at the MP2/6-311+G(d,p) level, the PES of the dimer corresponding to variations in chain separation and overlap was explored. Two minima on this surface were found, varying in their degree of overlap, but both having C 2 h symmetry. Topological charge density analysis shows these two arrangements to have qualitatively different structures. Atoms in Molecules decomposition shows the origin of the dimer stabilisation to lie in an increase in nitrogen's population and self-stabilisation.

Platts, James A.; Howard, Sean T.; Fallis, Ian. A.

1998-03-01

83

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

84

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

PubMed

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

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

2014-08-28

85

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

86

Quantum effects in intermediate-temperature dipole-dipole correlation-functions in the presence of an environment.  

PubMed

We study thermal dipole-dipole correlation functions and their corresponding IR spectra in the presence of an intermediate temperature bath of harmonic oscillators. Whereas for a Morse oscillator without coupling to a heat bath, the quantum level structure is displayed in the spectrum, classical calculations show a broad, smeared out spectrum. In the presence of purely Ohmic dissipation already for extremely weak relaxation rate, the classical case is recovered. Using the HEOM approach of Tanimura and Wolynes [Phys. Rev. A 43, 4131 (1991)], we show that to observe some remnants of the level structure in the spectrum for moderate damping strength as well as intermediate temperatures, the dynamics has to be non-Markovian (Ohmic dissipation with cutoff). PMID:25318720

Grossmann, F

2014-10-14

87

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

88

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

89

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

SciTech Connect

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

Yogesha, S.D.; SHarff, A.; Bricogne, G.; Izard, .T. (Globel Phasing); (Scripps)

2012-03-13

90

Ferroelectric ordering in chiral smectic-C* liquid crystals determined by nonchiral intermolecular interactions.  

PubMed

General microscopic mechanism of ferroelectric ordering in chiral smectic-C* liquid crystals is considered. It is shown that if the mesogenic molecules have a sufficiently low symmetry, the spontaneous polarization is proportional to one of the biaxial vector order parameters of the smectic-C phase. This order parameter may be determined by intermolecular interactions which are not sensitive to molecular chirality. At the same time, the polarization is also proportional to a pseudoscalar parameter which vanishes if the molecules are nonchiral. The general statistical theory of ferroelectric ordering is illustrated by two particular models. The first model is based on electrostatic quadrupole-quadrupole interactions, and it enables one to obtain explicit analytical expressions for the spontaneous polarization. In the second model, the molecular chirality and polarity are determined by a pair of off-center nonparallel dipoles. For this case, the spontaneous polarization is calculated numerically as a function of temperature. The theory provides a more general interpretation of the previous approaches including the classical Boulder model. PMID:18517400

Osipov, M A; Gorkunov, M V

2008-03-01

91

Anti-plasticizing effect of amorphous indomethacin induced by specific intermolecular interactions with PVA copolymer.  

PubMed

The mechanism of how poly(vinyl alcohol-co-acrylic acid-co-methyl methacrylate) (PVA copolymer) stabilizes an amorphous drug was investigated. Solid dispersions of PVA copolymer, poly(vinyl pyrrolidone) (PVP), and poly(vinyl pyrrolidone-co-vinyl acetate) (PVPVA) with indomethacin (IMC) were prepared. The glass transition temperature (Tg)-proportion profiles were evaluated by differential scanning calorimetry (DSC). General Tg profiles decreasing with the IMC ratio were observed for IMC-PVP and IMC-PVPVA samples. An interesting antiplasticizing effect of IMC on PVA copolymer was observed; Tg increased up to 20% IMC ratio. Further addition of IMC caused moderate reduction with positive deviation from theoretical values. Specific hydrophilic and hydrophobic interactions between IMC and PVA copolymer were revealed by infrared spectra. The indole amide of IMC played an important role in hydrogen bonding with PVA copolymer, but not with PVP and PVPVA. X-ray diffraction findings and the endotherm on DSC profiles suggested that PVA copolymer could form a semicrystalline structure and a possibility of correlation of the crystallographic nature with its low hygroscopicity was suggested. PVA copolymer was able to prevent crystallization of amorphous IMC through both low hygroscopicity and the formation of a specific intermolecular interaction compared with that with PVP and PVPVA. PMID:24890320

Ueda, Hiroshi; Aikawa, Shohei; Kashima, Yousuke; Kikuchi, Junko; Ida, Yasuo; Tanino, Tadatsugu; Kadota, Kazunori; Tozuka, Yuichi

2014-09-01

92

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

PubMed Central

Dhh1 is a highly conserved DEAD-box protein that has been implicated in many processes involved in mRNA regulation. At least some functions of Dhh1 may be carried out in cytoplasmic foci called processing bodies (P-bodies). Dhh1 was identified initially as a putative RNA helicase based solely on the presence of conserved helicase motifs found in the superfamily 2 (Sf2) of DEXD/H-box proteins. Although initial mutagenesis studies revealed that the signature DEAD-box motif is required for Dhh1 function in vivo, enzymatic (ATPase or helicase) or ATP binding activities of Dhh1 or those of any its many higher eukaryotic orthologues have not been described. Here we provide the first characterization of the biochemical activities of Dhh1. Dhh1 has weaker RNA-dependent ATPase activity than other well characterized DEAD-box helicases. We provide evidence that intermolecular interactions between the N- and C-terminal RecA-like helicase domains restrict its ATPase activity; mutation of residues mediating these interactions enhanced ATP hydrolysis. Interestingly, the interdomain interaction mutant displayed enhanced mRNA turnover, RNA binding, and recruitment into cytoplasmic foci in vivo compared with wild type Dhh1. Also, we demonstrate that the ATPase activity of Dhh1 is not required for it to be recruited into cytoplasmic foci, but it regulates its association with RNA in vivo. We hypothesize that the activity of Dhh1 is restricted by interdomain interactions, which can be regulated by cellular factors to impart stringent control over this very abundant RNA helicase. PMID:21642421

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

2011-01-01

93

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

NASA Astrophysics Data System (ADS)

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

Gu, Zhiyong

94

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

95

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

96

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

97

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

NASA Astrophysics Data System (ADS)

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

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

2007-10-01

98

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

PubMed

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. PMID:25134562

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

2014-08-14

99

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

100

Intermolecular interaction potentials of methane and ethylene dimers calculated with the Møller Plesset, coupled cluster and density functional methods  

NASA Astrophysics Data System (ADS)

Intermolecular interaction potentials of methane and ethylene dimers were calculated by the Hartree-Fock, Møller-Plesset, coupled cluster and density functional methods. The CCSD(T) electron correlation energies were close to the MP4(SDTQ) ones. The MP2 and MP3 energies were not largely different from the MP4(SDTQ) ones. On the other hand the CCSD and MP4(SDQ) methods largely underestimated the electron correlation energies. Dispersion interaction was not covered by the density functional methods using the BLYP, BPW91 and B3LYP functionals. These functionals also had defects in the evaluation of the repulsion interactions.

Tsuzuki, Seiji; Uchimaru, Tadafumi; Tanabe, Kazutoshi

1998-04-01

101

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

102

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...

103

Direction-dependent Intermolecular Interactions: Catechol on TiO2(110)-11  

E-print Network

is often used in solar energy conversion, where the material is adopted as the electrode in dye step edges is observed at room temperature. A statistical analysis of intermolecular distances-sensitized solar cells. [3-5] The band gap of TiO2 is ~3.2eV, located in the ultraviolet region. A monolayer

Diebold, Ulrike

104

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

E-print Network

Iodine Bonding Stabilizes Iodomethane in MIDAS Pesticide. Theoretical Study of Intermolecular of chloropicrin and iodomethane in the pesticide Midas is a good choice to reduce the volatility of iodomethane, methyl iodide, chloropicrin, pesticide, soil fumigant, UHF instability INTRODUCTION By the end of 2004

Glaser, Rainer

105

Luminescent goldI carbenes from 2-pyridylisocyanide complexes: structural consequences of intramolecular versus intermolecular hydrogen-bonding interactions.  

PubMed

Isocyanide [AuX(CNPy-2)] (X = Cl, C6F5, fluoromesityl, 1/2 octafluorobiphenyl) and carbene [AuX{C(NR1R2)(NHPy-2)}] (R1R2NH = primary or secondary amines or 1/2 primary diamine) gold(I) complexes have been synthesized and characterized. For X = Cl, the carbene complexes show aurophilic interactions. The fragment NHPy-2, formed in the carbenes, can give rise to intra- (for primary amines) or intermolecular (for secondary amines) hydrogen bonds, depending on the amine used. These bonds and contacts have been studied in the solid state and in solution. The intermolecular hydrogen bonds are split in an acetone solution, but the intramolecular ones, which close a six-membered ring, survive in solution. Except for the fluoromesityl derivatives, the carbene complexes display luminescent properties. PMID:18237121

Bartolomé, Camino; Carrasco-Rando, Marta; Coco, Silverio; Cordovilla, Carlos; Martín-Alvarez, Jose M; Espinet, Pablo

2008-03-01

106

An anomalous dipole-dipole arrangement of water molecules encapsulated into C60 dimer  

NASA Astrophysics Data System (ADS)

Based on first-principles total energy calculations, we demonstrate that two water molecules encapsulated in the C60 dimer form a peculiar tail-to-tail dipole arrangement that is energetically unfavorable in classical electrodynamics. This arrangement is ascribed to charge depression at the wall of C60 associated with [2 + 2] cycloaddition in the dimer structure resulting in a decrease of the energy cost of Coulomb repulsive interaction in the arrangement. First-principles molecular dynamics simulations also show that the water molecules retain the peculiar arrangement up to the temperature of about 10 K.

Nomura, Kazuya; Okada, Susumu

2014-07-01

107

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.  

PubMed

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods. PMID:20604521

Czyznikowska, Z; Góra, R W; Zale?ny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

108

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

109

Tailoring intermolecular interactions for efficient room-temperature phosphorescence from purely organic materials in amorphous polymer matrices.  

PubMed

Herein we report a rational design strategy for tailoring intermolecular interactions to enhance room-temperature phosphorescence from purely organic materials in amorphous matrices at ambient conditions. The built-in strong halogen and hydrogen bonding between the newly developed phosphor G1 and the poly(vinyl alcohol) (PVA) matrix efficiently suppresses vibrational dissipation and thus enables bright room-temperature phosphorescence (RTP) with quantum yields reaching 24?%. Furthermore, we found that modulation of the strength of halogen and hydrogen bonding in the G1-PVA system by water molecules produced unique reversible phosphorescence-to-fluorescence switching behavior. This unique system can be utilized as a ratiometric water sensor. PMID:25044368

Kwon, Min Sang; Lee, Dongwook; Seo, Sungbaek; Jung, Jaehun; Kim, Jinsang

2014-10-13

110

Intermolecular interaction in the H2S-H2 complex: molecular beam scattering experiments and ab-inito calculations.  

PubMed

New molecular beam scattering experiments are reported for the H2S-H2 system recording, under high angular and velocity resolution conditions, the "glory" quantum interference in the velocity dependence of the total cross section. The analysis of the experimental data permits the determination, for the first time, of a spherically averaged intermolecular potential for this system. An evaluation of significant cuts of the potential energy surface, obtained by accurate ab initio CCSD(T) calculations using large basis sets, combined with the analysis of the electronic charge displacement accompanying the formation of H2S-H2, has been also performed in order to rationalize the experimental findings. A direct comparison with the analogous water-hydrogen complex (Belpassi, L. et al. J. Am. Chem. Soc. 2010, 132, 13046), investigated with the same experimental conditions and theoretical methodology, brings to light detailed differences in the intermolecular interaction affecting the observables. In particular, it shows the important fact that the charge transfer (CT) component of the interaction plays a minor role in H2S-H2, whereas it was found to be a crucial stabilization component of the interaction in water-H2, determining the potential energy surface anisotropy and the precise location of the energy minima. PMID:24716742

Bartocci, Alessio; Cappelletti, David; Pirani, Fernando; Tarantelli, Francesco; Belpassi, Leonardo

2014-08-21

111

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; Zo?ek, Teresa; Wolska, Irena; Maciejewska, Dorota

2014-10-01

112

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; Zolek, Teresa; Wolska, Irena; Maciejewska, Dorota

2014-01-01

113

Insight on the interaction of polychlorobiphenyl with nucleic acid-base.  

PubMed

The interaction between one polychlorobiphenyl (3,3',4,4',-tetrachlorobiphenyl, coded PCB77) and the four DNA nucleic acid-base is studied by means of quantum mechanics calculations in stacked conformations. It is shown that even if the intermolecular dispersion energy is the largest component of the total interaction energy, some other contributions play a non negligible role. In particular the electrostatic dipole-dipole interaction and the charge transfer from the nucleobase to the PCB are responsible for the relative orientation of the monomers in the complexes. In addition, the charge transfer tends to flatten the PCB, which could therefore intercalate more easily between DNA base pairs. From these seminal results, we predict that PCB could intercalate completely between two base pairs, preferably between Guanine:Cytosine pairs. PMID:22972692

Abtouche, Soraya; Very, Thibaut; Monari, Antonio; Brahimi, Meziane; Assfeld, Xavier

2013-02-01

114

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

PubMed

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

Korona, Tatiana

2008-06-14

115

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

116

Noncovalent cation-? interactions - their role in nature.  

PubMed

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

Fink, Krzysztof; Boraty?ski, Janusz

2014-01-01

117

Probing the dependence of long-range, four-atom interactions on intermolecular orientation: 3. Hydrogen and iodine.  

PubMed

Two-laser, action spectroscopy experiments have been performed in the I(2)B-X, ?'-0 spectral region on H(2)···I(2) and D(2)···I(2) complexes to investigate the dependence of the H(2)/D(2) + I(2) intermolecular interactions on orientation. The spectra contain features associated with at least two different conformers of the ground-state H(2)/D(2)···I(2)(X,?'' = 0) complexes; one conformer has a preferred T-shaped geometry with the H(2)/D(2) moiety localized in a potential minimum that is orthogonal to the I-I bond axis, and the second conformer has a linear geometry with the H(2)/D(2) moiety positioned in minima at either end of the I(2) molecule, along the bond axis. Those features associated with complexes containing para-H(2)(j = 0), ortho-H(2)(j = 1), ortho-D(2)(j = 0), and para-D(2)(j = 1) are also assigned. The linear conformers are found to be more strongly bound than the T-shaped conformers with binding energies of 118.9(1.9) cm(-1) versus 91.3-93.3 cm(-1) for the ortho-H(2)···I(2) complexes and 144.2(2.1) cm(-1) versus 107.9 cm(-1) for the para-D(2)···I(2) complexes, respectively. Electronic structure calculations of the complexes containing ICl and I(2) with H(2), He, Ne, and Ar were performed to reveal the nature of the interactions and to shed insight into the origins of the different binding energies. The most stable minima in the H(2)/D(2) + I(2)(B,?') excited-state potentials have T-shaped geometries. Calculated energies and probability amplitudes of the excited-state levels provide insight into the different excited-state intermolecular vibrational levels accessed by transitions of the two ground-state conformers. PMID:21568302

Darr, Joshua P; Loomis, Richard A; Ray-Helmus, Sara E; McCoy, Anne B

2011-06-30

118

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

119

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

120

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

121

Local electron correlation descriptions of the intermolecular stacking interactions between aromatic intercalators and nucleic acids  

NASA Astrophysics Data System (ADS)

Interaction energies for the binding of three intercalators to nucleic acid base pairs and base-pair steps are presented. Density fitting (DF) and local (L) correlation methods are employed, allowing use of basis sets appropriate for description of non-covalent interactions. In common with previous studies of stacking interactions, DF-LMP2 overestimates binding by as much as 50%. However, spin-component scaling (SCS) corrects for this effect, resulting in binding energies that support literature data obtained with small basis sets and/or density functional theory. The efficiency of this approach allows intercalators within base-pair steps to be studied, revealing substantial many body terms.

Grant Hill, J.; Platts, James A.

2009-09-01

122

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

Microsoft Academic Search

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

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

2000-01-01

123

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

SciTech Connect

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

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

2000-11-01

124

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

E-print Network

exchange response kernel are tested on rare-gas dimers and the S22 benchmark set of weakly interacting [22], coupled-cluster theory [23] or multi-reference second-order perturbation theory [24]. Recently

125

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

126

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

PubMed

Two cycloimmonium ylids with pyridinium and iso-quinolinium as heterocycle and having common carbanion were studied from the point of view of the solvent influence on electronic absorption spectra in binary and ternary solutions. The supplies of the universal and specific interactions to the spectral shifts in the electronic absorption spectra of hydroxyl solutions were separated. The strength of the specific interactions of the ylid molecules with octanol was estimated by using ternary solutions in binary solvent Octanol+Dichloroethane, in which the universal interactions have similar strengths. Quantum mechanical calculations and also the solvatochromic effect allowed us estimating the values of the molecular dipole moments in the excited state of the studied ylids. The conclusions showed that by excitation the molecular dipole moment of the studied ylids decreases or changes its sense, due to the electronic charge transport from the carbanion towards the heterocycle. PMID:24342294

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

2014-03-25

127

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

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

128

Gels from a semifluorinated n-alkane in fluorinated solvents as a probe for intermolecular interactions.  

PubMed

Diblock semifluorinated n-alkanes can form aggregates and gels in fluorinated solvents. We have investigated the thermal behavior of binary mixtures comprising F(CF(2))(8)(CH(2))(16)H and fluorinated solvents. The solvents were perfluorohexane, perfluoroheptane, perfluorooctane, perfluorooctyl bromide, perfluorodecalin, and perfluorotributylamine. The phase diagrams were used to calculate the activity coefficients of the two components and the main excess thermodynamic functions. The solubility and self-assembly behavior of F(8)H(16) in the fluorinated solvents are related to the different solute-solvent dispersion interactions that depend on the polarizabilities and ionization potentials of the interacting species, and on the structural properties of the solvent. PMID:19682704

Tattini, Lorenzo; Lo Nostro, Pierandrea; Scalise, Luca; Ninham, Barry W; Baglioni, Piero

2009-11-01

129

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

130

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

131

Intermolecular interaction studies in ammonium squarate: crystal structure and vibrational spectra  

NASA Astrophysics Data System (ADS)

Ammonium squarate salt [(NH 4) 2C 4O 4] crystallizes in the monoclinic space group P2 1/c. The crystal presents the squarate ions displayed in layers parallel to a crystallographic axis and forming hydrogen bonds interactions with NH4+ cations, localized between squarate anions layers. The squarate anion presents similar CC and CO bond distances which indicate a degree of electronic delocalization in the rings. A ?-stacking interaction is observed between squarate rings separated by interplanar distance and centroid ring distance of respectively 3.41 and 3.71 Å. The electron delocalization was also observed in the vibrational spectra. The infrared spectrum shows a narrow band around 1530 cm -1, assigned to a coupled stretching mode of CO and CC groups, indicating the high symmetry of the squarate ion. The Raman spectrum also shows this effect in the 1000 to 1200 cm -1 region (related to CC stretching mode), where it is expected a decrease of the number of bands if compared to squarate ion in aqueous solution, where the symmetry is actually D4 h; in the (NH 4) 2C 4O 4 Raman spectrum just one strong band is observed at 1120 cm -1. All the vibrational results indicate the symmetry is very close to the one observed for the solvated ion in aqueous solution; once again the vibrational analysis appears as an important tool in recognizing the oxocarbon ion geometry in the solid state.

Georgopoulos, Stéfanos L.; Diniz, Renata; Rodrigues, Bernardo L.; Yoshida, Maria I.; de Oliveira, Luiz Fernando C.

2005-10-01

132

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

133

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

134

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

PubMed Central

Receptor tyrosine kinase (RTK) signaling is spatially and temporally regulated by a number of positive and negative regulatory mechanisms. These regulatory mechanisms control the amplitude and duration of the signals initiated at the cell surface to have a normal or aberrant biological outcome in development and disease, respectively. In the past decade, the Sprouty (Spry) family of proteins has been identified as modulators of RTK signaling in normal development and disease. This review summarizes recent advances concerning the biological activities modulated by Spry family proteins, their interactions with signaling proteins, and their involvement in cardiovascular diseases and cancer. The diversity of mechanisms in the regulation of Spry expression and activity in cell systems emphasizes the crucial role of Spry proteins in development and growth across the animal kingdom. PMID:19570949

Edwin, Francis; Anderson, Kimberly; Ying, Chunyi

2009-01-01

135

Theoretical analysis of the intermolecular interactions in naphthalene diimide and pyrene complexes.  

PubMed

Supramolecular assembly of donor-acceptor complexes as the key component in organic functional nanomaterials is a promising approach for future electronic devices. One representative example of the donor-acceptor complexes is the naphthalene diimide-pyrene (NDI-Py) system, which shows fascinating photoelectric properties. Herein, the analysis of the ?-? interactions between NDI and Py has been investigated using the DFT/M06-2X and reduced density gradient methods. According to the calculations, the attractive forces for the stabilization of the NDI-Py dimer are dependent on the rotation angles, which provide physical insight into the experimental data reported by Wilson and co-workers (Langmuir, 2011, 27, 6554). Our results not only provide computational evidence for the origin of the rotation in the crystal structure of the NDI-Py but also address the role of the charge-transfer attractions in the complexes. PMID:25294626

Yeh, Mei-Yu; Lin, Hsin-Chieh

2014-10-21

136

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

PubMed Central

The structure of the title diterpenoid, C20H28O3, {systematic name: (4bS,8aS)-3-hy­droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa­hydro­phenanthrene-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 cyclo­hexane ring adopts a chair conformation whereas the other cyclo­hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra­molecular O—H?O hydrogen bond generates an S(5) ring motif. In the crystal, mol­ecules are linked into chains along [010] by O—H?O hydrogen bonds and weak C—H?O inter­actions. 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

2011-01-01

137

Exploring contribution of intermolecular interactions in supramolecular layered assembly of naphthyridine co-crystals: Insights from Hirshfeld surface analysis of their crystalline states  

NASA Astrophysics Data System (ADS)

Co-crystals of 1a and 1b have been prepared by slow evaporation of the solutions of mixtures of 2,7-dimethyl-1,8-naphthyridine (1), urea (a) and thiourea (b). The structures of the complexes are determined by the single crystal X-ray diffraction and a detailed investigation of the crystal packing and classification of intermolecular interactions is presented by means of Hirshfeld surface analysis which is of considerable current interest in crystal engineering. The X-ray study reveals that the co-crystal formers are envisioned to produce N-H⋯N hydrogen bond as well as N-H⋯O/N-H⋯S pair-wise hydrogen bonds and also the weaker aromatic ?⋯? interactions which cooperatively take part in the crystal packing. The recurring feature of the self-assembly in the compounds is the appearance of the molecular ribbon through multiple hydrogen bonding which are further stacked into molecular layers by ?⋯? stacking interactions. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D Fingerprint plots have been used to examine molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

Seth, Saikat Kumar; Das, Nirmal Kumar; Aich, Krishnendu; Sen, Debabrata; Fun, Hoong-Kun; Goswami, Shyamaprasad

2013-09-01

138

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

139

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

PubMed

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

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

2011-08-01

140

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

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

141

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

SciTech Connect

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

Azar, R. Julian; Head-Gordon, Martin [Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720 (United States) and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

2012-01-14

142

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

Microsoft Academic Search

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

Konstantin Pervushin; Roland Riek; Gerhard Wider; Kurt Wuthrich

1997-01-01

143

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

PubMed Central

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

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

2010-01-01

144

Intermolecular Interactions and the Nature of Orientational Ordering in the Solid Fullerenes C60 and C70  

Microsoft Academic Search

We have proposed an intermolecular potential for C60 molecules that not only reproduces the correct low-temperature structure, but also correlates a wide range of experimental properties, including the molecular reorientational time in the room-temperature rotator phase, the volume change at the orientational ordering transition, and the librational frequencies in the low-temperature phase. The low-pressure phases in solid C70 have been

Ailan Cheng; Michael Klein; Michele Parrinello; Michiel Sprik

1992-01-01

145

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

NASA Astrophysics Data System (ADS)

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

Marino, Michele; Vairo, Giuseppe

2014-12-01

146

Effects of the higher electron correlation correction on the calculated intermolecular interaction energies of benzene and naphthalene dimers: comparison between MP2 and CCSD(T) calculations  

NASA Astrophysics Data System (ADS)

Intermolecular interaction energies of parallel and T-shape benzene dimers and parallel naphthalene dimer were calculated with MP2, MP3, MP4(SDQ), MP4(SDTQ), CCSD and CCSD(T) electron correlation corrections using several basis sets. The MP2 calculations considerably overestimated the attraction compared to the CCSD(T) ones. The MP2 correlation interaction energies, the differences between the HF and MP2 interaction energies, were 21-38% larger than the corresponding CCSD(T) ones. The MP4(SDQ) and CCSD calculations substantially underestimated the attraction compared to MP4(SDTQ) and CCSD(T), which indicated the importance of triple excitation. The estimated CCSD(T) interaction energies of the three dimers with reasonably large basis sets were -1.74, -2.50 and -5.69 kcal/mol, respectively.

Tsuzuki, Seiji; Uchimaru, Tadafumi; Matsumura, Kazunari; Mikami, Masuhiro; Tanabe, Kazutoshi

2000-03-01

147

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

148

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

PubMed

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

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

2013-06-01

149

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

150

Intra- and intermolecular Se···X (X = Se, O) interactions in selenium-containing heterocycles: 3-benzoylimino-5-(morpholin-4-yl)-1,2,4-diselenazole.  

PubMed

In the selenium-containing heterocyclic title compound {systematic name: N-[5-(morpholin-4-yl)-3H-1,2,4-diselenazol-3-ylidene]benzamide}, C13H13N3O2Se2, the five-membered 1,2,4-diselenazole ring and the amide group form a planar unit, but the phenyl ring plane is twisted by 22.12 (19)° relative to this plane. The five consecutive N-C bond lengths are all of similar lengths [1.316 (6)-1.358 (6) Å], indicating substantial delocalization along these bonds. The Se···O distance of 2.302 (3) Å, combined with a longer than usual amide C=O bond of 2.252 (5) Å, suggest a significant interaction between the amide O atom and its adjacent Se atom. An analysis of related structures containing an Se-Se···X unit (X = Se, S, O) shows a strong correlation between the Se-Se bond length and the strength of the Se···X interaction. When X = O, the strength of the Se···O interaction also correlates with the carbonyl C=O bond length. Weak intermolecular Se···Se, Se···O, C-H···O, C-H···? and ?-? interactions each serve to link the molecules into ribbons or chains, with the C-H···O motif being a double helix, while the combination of all interactions generates the overall three-dimensional supramolecular framework. PMID:24816018

Linden, Anthony; Zhou, Yuehui; Heimgartner, Heinz

2014-05-01

151

The interaction of atoms in layers adsorbed on graphene  

NASA Astrophysics Data System (ADS)

Adsorption on single-layer graphene at finite adatom concentrations is considered within the surface-molecule model. The main channels of adatom interaction (dipole-dipole repulsion and exchange) are taken into account. It is shown that the consideration of interaction leads to adatom depolarization.

Davydov, S. Yu.

2014-07-01

152

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, Julio Cesar; Sforca, Mauricio Luis; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jorg

2013-01-01

153

Penning ionization of N2O molecules by He*(2(3,1)S) and Ne*(3P2,0) metastable atoms: theoretical considerations about the intermolecular interactions.  

PubMed

A theoretical investigation of the intermolecular interaction, operative in collision complexes of He*(2 3S1), He*(2 1S0), and Ne*(3P2,0) with N2O, is carried out to explain the main results of the experimental study reported in the preceding paper. The analysis is carried out by means of a semiempirical method based on the identification, modeling, and combination of the leading interaction components, including the effect of the selective polarization of the more external electronic cloud of the metastable atom in the intermolecular electric field. These and other crucial aspects of our approach have been quantitatively verified by ab initio calculations. The proposed method permits to evaluate the interaction at any configuration of the complexes and provides a useful and inexpensive representation of the intermolecular potential energy for dynamics studies. The main experimental findings can be rationalized taking into account the critical balancing between molecular orientation effects in the intermolecular interaction field and the ionization probability. These orientation effects tend to become less pronounced with increasing collision energy. PMID:15945685

Biondini, Francesco; Brunetti, Brunetto G; Candori, Pietro; De Angelis, Filippo; Falcinelli, Stefano; Tarantelli, Francesco; Pirani, Fernando; Vecchiocattivi, Franco

2005-04-22

154

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

155

Molecular characterization and intermolecular interaction of coat protein of Prunus necrotic ringspot virus: implications for virus assembly.  

PubMed

Coat protein (CP) and RNA3 from Prunus necrotic ringspot virus (PNRSV-rose), the most prevalent virus infecting rose in India, were characterized and regions in the coat protein important for self-interaction, during dimer formation were identified. The sequence analysis of CP and partial RNA 3 revealed that the rose isolate of PNRSV in India belongs to PV-32 group of PNRSV isolates. Apart from the already established group specific features of PV-32 group member's additional group-specific and host specific features were also identified. Presence of methionine at position 90 in the amino acid sequence alignment of PNRSV CP gene (belonging to PV-32 group) was identified as the specific conserved feature for the rose isolates of PNRSV. As protein-protein interaction plays a vital role in the infection process, an attempt was made to identify the portions of PNRSV CP responsible for self-interaction using yeast two-hybrid system. It was found (after analysis of the deletion clones) that the C-terminal region of PNRSV CP (amino acids 153-226) plays a vital role in this interaction during dimer formation. N-terminal of PNRSV CP is previously known to be involved in CP-RNA interactions, but our results also suggested that N-terminal of PNRSV CP represented by amino acids 1-77 also interacts with C-terminal (amino acids 153-226) in yeast two-hybrid system, suggesting its probable involvement in the CP-CP interaction. PMID:24426281

Kulshrestha, Saurabh; Hallan, Vipin; Sharma, Anshul; Seth, Chandrika Attri; Chauhan, Anjali; Zaidi, Aijaz Asghar

2013-09-01

156

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

157

A new kind of intermolecular stacking interaction between copper (II) mixed chelate complex (Casiopeína III-ia) and adenine  

Microsoft Academic Search

Casiopeínas® are Cu (II) mixed chelate complexes that have shown cytotoxic, genotoxic and antineoplastic activity. In order to understand the interaction of these complexes with biomolecules, we have studied in this work the interaction of Casiopeína III-ia [CAS 223930-33-4] with adenine, cytosine, thymine and guanine. X-ray diffraction analysis shown the molecular structure of an adduct {[Cu(dmbipy)(acac)(H2O)]NO3(adenine)2·2H2O} where dmbipy=4,4?-dimethyl-2,2?-bipyridyne and acac=acetylacetonate,

Juan Carlos García-Ramos; Araceli Tovar-Tovar; Joseelyne Hernández-Lima; Fernando Cortés-Guzmán; Rafael Moreno-Esparza; Lena Ruiz-Azuara

2011-01-01

158

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

159

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

NASA Astrophysics Data System (ADS)

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

Lao, Ka Un; Herbert, John M.

2013-06-01

160

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

161

Interaction energy contributions of H-bonded and stacked structures of the AT and GC DNA base pairs from the combined density functional theory and intermolecular perturbation theory approach.  

PubMed

Stacked and Watson-Crick structures of DNA base pairs are investigated with the DFT-SAPT variant of intermolecular perturbation theory, yielding a rigorous decomposition of the interaction energy into electrostatic, induction, dispersion, and exchange contributions. Their interplay in the various structures is analyzed. Total interaction energies extrapolated to the complete basis set limit are compared with corresponding second-order Møller-Plesset and estimated coupled-cluster theory results. PMID:16953592

Hesselmann, Andreas; Jansen, Georg; Schütz, Martin

2006-09-13

162

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

163

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

PubMed

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

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

2013-11-01

164

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

165

Controlling gold atom penetration through alkanethiolate self-assembled monolayers on Au{111} by adjusting terminal group intermolecular interactions.  

PubMed

The penetration behavior of thermally evaporated Au on S(CH(2))(15)CH(3), S(CH(2))(15)CO(2)CH(3), S(CH(2))(15)CO(2)H, K-modified S(CH(2))(15)CO(2)CH(3), and K-modified S(CH(2))(15)CO(2)H self-assembled monolayers (SAM) on Au substrates is investigated. Gold is a particularly interesting metal since vapor-deposited Au atoms are known to pass through alkanethiolate SAMs on Au{111} substrates at room temperature. Here we show that it is possible to control Au penetration by adjusting the interactions between terminal groups. It is found that Au atoms evenly penetrate into the CH(3) and CO(2)CH(3) films, forming smooth buried layers below the organic thin films. For the CO(2)H film, although Au atoms can still penetrate through it, filaments and mushroomlike clusters form due to H-bonding between film molecules. In the case of the K-modified CO(2)CH(3) or CO(2)H films, however, most Au atoms form islands at the vacuum interface. These results suggest that van der Waals forces and H-bonds are not strong enough to block Au from going through but that ionic interactions are able to block Au penetration. The measurements were performed primarily using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and atomic force microscopy (AFM). The combination of these highly complementary probes provides a very useful strategy for the study of metal atom behavior on SAMs. PMID:17044698

Zhu, Zihua; Daniel, Thomas A; Maitani, Masato; Cabarcos, Orlando M; Allara, David L; Winograd, Nicholas

2006-10-25

166

The CH-? Interactions of Methyl Ethers as a Model for Carbohydrate-N-Heteroarene Interactions.  

PubMed

CH-? interactions have been cited as an important contributor to carbohydrate recognition. To determine whether N-heterocycles form stronger CH-? interactions, the interactions of methyl ether groups with heterocyclic and nonheterocyclic aromatic surfaces were studied. Both experimental and computational experiments found that N-heterocyclic aromatic surfaces formed stronger interactions. This enhancement was attributed to attractive dipole-dipole interactions between the methyl ether C-O bond and the N-heterocyclic aromatic dipole. PMID:25238038

Li, Ping; Parker, Trent M; Hwang, Jungwun; Deng, Fengyuan; Smith, Mark D; Pellechia, Perry J; Sherrill, C David; Shimizu, Ken D

2014-10-01

167

The van der Waals Interaction of Hydrogen Atoms  

Microsoft Academic Search

The van der Waals interaction energy of two hydrogen atoms at large internuclear distances is discussed by the use of a linear variation function. By including in the variation function, in addition to the unperturbed wave function, 26 terms for the dipole-dipole interaction, 17 for the dipole-quadrupole interaction, and 26 for the quadrupole-quadrupole interaction, the interaction energy is evaluated as

Linus Pauling; J. Y. Beach

1935-01-01

168

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

169

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

170

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

171

Competing magnetic interactions in quantum thin films  

NASA Astrophysics Data System (ADS)

In this work we study the quantum spin-1/2 Heisenberg model in two dimensions, with a nearest-neighbor short-range antiferromagnetic exchange (J) and a long-range ferromagnetic dipole-dipole (Ed) coupling. Using the double-time Green's function method within the random phase approximation (RPA) we obtain the magnon dispersion relation as function of frustration parameter ? (? being the ratio between exchange and dipolar interactions ?=J/Ed). We study the competition between long-range ferromagnetic dipole-dipole interaction and short-range antiferromagnetic exchange in stabilizing the magnetic long-range order in a two-dimensional system. We find that the ferromagnetic order is stable at small k up to critical value of frustration ?c=0.04375. For frustration higher than the critical value (?>?c) our magnetic system is disordered.

Bueno, M. J.; Faria, Jorge L. B.; de Arruda, Alberto S.; Craco, L.; de Sousa, J. Ricardo

2013-07-01

172

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

SciTech Connect

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

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

1991-12-31

173

Desensitization of metastable intermolecular composites  

DOEpatents

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

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

2011-04-26

174

C-NOT gate based on ultracold Rydberg atom interactions  

NASA Astrophysics Data System (ADS)

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

Rashid, Muhammad; Maarten, Hoogerland; Yasir, Jamil

2013-11-01

175

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

176

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

177

Poly[(?-pentafluorobenzoato-?(2)O:O')(pentafluorobenzoato-?O)(?-pyrazine-?(2)N: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

2014-11-15

178

Resonance interaction induced by metal surfaces catalyzes atom-pair breakage  

NASA Astrophysics Data System (ADS)

We present the theory for retarded resonance interaction between two identical atoms at arbitrary positions near a metal surface. The dipole-dipole resonance interaction force that binds isotropically excited atom pairs together in free space may turn repulsive close to an ideal (totally reflecting) metal surface. On the other hand, close to an infinitely permeable surface it may turn more attractive. We illustrate numerically how the dipole-dipole resonance interaction between two oxygen atoms near a metal surface may provide a repulsive energy of the same order of magnitude as the ground-state binding energy of an oxygen molecule. As a complement we also present results from density-functional theory.

Boström, Mathias; Persson, Clas; Ninham, Barry W.; Norman, Patrick; Sernelius, Bo E.

2013-04-01

179

Investigation of intermolecular hydrogen bond interactions in crystalline L-cysteine by DFT calculations of the oxygen-17, nitrogen-14, and hydrogen-2 EFG tensors and AIM analysis.  

PubMed

A systematic computational study is carried out to investigate hydrogen bond (HB) interactions in the real crystalline structures of L-cysteine at 30 and 298 K by density functional theory (DFT) calculations of electric field gradient (EFG) tensors at the sites of O-17, N-14, and H-2 nuclei. One-molecule (monomer) and nine-molecule (cluster) models of L-cysteine are created by available crystal coordinates at both temperatures and the EFG tensors are calculated for both models to indicate the effect of HB interactions on the tensors. The calculated EFG tensors at the level of B3LYP and B3PW91 DFT methods and 6-311++G** and cc-pVTZ basis sets are converted to those experimentally measurable nuclear quadrupole resonance (NQR) parameters i.e. quadrupole coupling constants (qcc) and asymmetry parameters (eta(Q)). The evaluated NQR parameters reveal that the EFG tensors of (17)O, (14)N, and (2)H are influenced and show particular trends from monomer to the target molecule in the cluster due to the contribution of target molecule to classic N-H...O, and non-classic S-H...O and S-H...S types of HB interactions. On the other hand, atoms in molecules (AIM) analyses confirm the presence of HB interactions and rationalize the observed EFG trends. The results indicate different contribution of various nuclei to HB interactions in the cluster where O2 and N1 have major contributions. The EFG tensors as well as AIM analysis at the H6 site show that the N1-H6...O2 HB undergoes a significant change from 30 to 298 K where changes in other N-H...O interactions are almost negligible. There is a good agreement between the calculated (14)N NQR parameters and reported experimental data. PMID:19168275

Nozad, Ahmad G; Meftah, Sakineh; Ghasemi, Mohammad H; Kiyani, Roya A; Aghazadeh, Mustafa

2009-04-01

180

Coherent Control of Atom-Atom Interactions and Entanglement using Optical Fields  

E-print Network

Two-photon optical transitions combined with long-range dipole-dipole interactions can be used for the coherent manipulation of collective metastable states composed of different atoms. We show that it is possible to induce optical resonances accompanied by the generation of entangled superpositions of the atomic states. Resonances of this kind can be used to implement quantum logic gates using optically excited single atoms (impurities) in the condensed phase.

M. D. Lukin; P. R. Hemmer

1999-05-07

181

Redetermined structure of diphenyl-phospho-nimidotriphenyl-phospho-rane: location of the hydrogen atoms and analysis of the inter-molecular inter-actions  

PubMed Central

The title compound, C30H25NOP2, is a bulky phosphazene derivative. Its previous crystal structure [Cameron et al. (1979 ?). Acta Cryst. B35, 1373–1377] is confirmed and its H atoms have been located in the present study. The formal P=N double bond is about 0.05?Å shorter than the P—N single bond and the large P=N—P bond angle reflects the steric strain in the mol­ecule. An intra­molecular C—H?O inter­action occurs. In the crystal, short C—H?O contacts connect the mol­ecules into chains propagating in [011], which are cross-linked via C—H?? inter­actions, generating a three-dimensional network. Aromatic ?–? stacking also occurs [shortest centroid–centroid separation = 3.6012?(11)?Å]. PMID:21754359

Betz, Richard; Gerber, Thomas; Hosten, Eric; Schalekamp, Henk

2011-01-01

182

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

PubMed Central

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

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

1998-01-01

183

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

PubMed Central

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

2013-01-01

184

Intermolecular potential energy surfaces for the interaction between H2X (Xdbnd O, S) and a metastable Ne*(3P2,0) atom  

NASA Astrophysics Data System (ADS)

Potential energy surfaces for the interaction of a Ne*(3P2,0) atom with H2O and H2S molecules are obtained on the basis of a semi empirical method that has been previously used for some specific orientations in Ne*(3P2,0)-H2O system. The method is now suitable for all orientations and also for Ne*(3P2,0)-H2S system. Interesting features emerge by comparing the two systems and appear related to different characteristics of the two molecular partners. The potential energy surface for Ne*(3P2,0)-H2S has been also successfully tested for reproducing recent experimental Penning ionization electron spectroscopy data, sensible to some specific orientations of the two colliding partners.

Falcinelli, Stefano; Bartocci, Alessio; Candori, Pietro; Pirani, Fernando; Vecchiocattivi, Franco

2014-10-01

185

Energetics of intermolecular HONO formation in condensed-phase  

E-print Network

; there is a very weak hydrogen-bonding-like interaction from the C­H of the CH2 group of one molecule to the O.O. Box 24658, Provo, Utah 84602-4658, USA Received 24 January 2003; in final form 20 February 2003 polymorphic phases. Our results show that the energetics of the intermolecular hydrogen transfer (to form HONO

Utah, University of

186

A Simple Demonstration of How Intermolecular Forces Make DNA Helical  

NASA Astrophysics Data System (ADS)

The DNA double helix provides a beautiful and easy to understand example of how intermolecular forces combine to determine macromolecular structure. A simple consideration of hydrogen bonds, dispersion forces, and ionic interactions explains why DNA is most stable as a helix. A model easily made from boxes and string illustrates the principles clearly. I present this demonstration to my general chemistry students after intermolecular forces have been introduced. The model may also be used in more advanced classes to explain how intercalators, such as ethidium bromide, unwind DNA when they wedge between base pairs.

Bruist, Michael F.

1998-01-01

187

Effects of impurity and Bose-Fermi interactions on the transition temperature of a dilute dipolar Bose-Einstein condensation in trapped Bose-Fermi mixtures  

NASA Astrophysics Data System (ADS)

The effects of impurity and Bose-Fermi interactions on the transition temperature of a dipolar Bose-Einstein condensation in trapped Bose-Fermi mixture, by using the two-fluid model, are investigated. The shift of the transition temperature consists of four contributions due to contact, Bose-Fermi, dipole-dipole, and impurity interactions. We will show that in the presence of an anisotropic trap, the Bose-Fermi correction to the shift of transition temperature due to the excitation spectra of the thermal part is independent of anisotropy factor. Applying our results to trapped Bose-Fermi mixtures shows that, by knowing the impurity effect, the shift of the transition temperature due to Bose-Fermi interaction could be measured for isotropic trap (dipole-dipole contributions is zero) and Feshbach resonance technique (contact potential contribution is negligible).

Yavari, H.; Mokhtari, M.

2014-03-01

188

Bulk and molecular compressibilities of organic-inorganic hybrids [(CH?)?N]?MnX? (X = Cl, Br); role of intermolecular interactions.  

PubMed

This work reports an X-ray diffraction, X-ray absorption, and Raman spectroscopy study of [(CH?)?N]?MnX? (X = Cl, Br) under pressure. We show that both compounds share a similar phase diagram with pressure. A P2?/c monoclinic structure describes precisely the [(CH?)?N]?MnCl? crystal in the 0.1-6 GPa range, prior to crystal decomposition and amorphization, while [(CH?)?N]?MnBr? can be described by a Pmcn orthorhombic structure in its stability pressure range of 0-3 GPa. These materials are attractive systems for pressure studies since they are readily compressible through the weak interaction between organic/inorganic [(CH?)?N?/MnX?²?] tetrahedra through hydrogen bonds and contrast with the small compressibility of both tetrahedra. Here we determine the equation-of-state (EOS) of each crystal and compare it with the corresponding local EOS of the MnX?²? and (CH?)?N? tetrahedra, the compressibility of which is an order and 2 orders of magnitude smaller than the crystal compressibility, respectively, in both chloride and bromide. The variations of the Mn-Cl bond distance obtained by extended X-ray absorption fine structure and the frequency of the totally symmetric ??(A?) Raman mode of MnCl?²? with pressure in [(CH?)?N]?MnCl? allowed us to determine the associated Grüneisen parameter (?(loc) = 1.15) and hence an accurate local EOS. On the basis of a local compressibility model, we obtained the Grüneisen parameters and corresponding variations of the intramolecular Mn–Br and C–N bond distances of MnBr?²? (?(loc) = 1.45) and (CH?)?N? (?(loc) = 3.0) in [(CH?)?N]?MnBr?. PMID:25244664

Barreda-Argüeso, Jose Antonio; Nataf, Lucie; Rodríguez-Lazcano, Yamilet; Aguado, Fernando; González, Jesús; Valiente, Rafael; Rodríguez, Fernando; Wilhelm, Heribert; Jephcoat, Andrew P

2014-10-01

189

Collective Many-Body Interaction in Rydberg Dressed Atoms  

SciTech Connect

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

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

2010-10-15

190

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

191

Intermolecular Interaction Studies of Winter Flounder  

E-print Network

, CA 95616 7 Department of Food Science and Technology, University of California, Davis, CA 95616 of action of AFP. The relevance of these findings to the mechanism of function of freezing inhibition and therefore the fish's blood serum falls well below freezing.1,2 It has been determined that the unusually low

Nguyen, Dat H.

192

Morphology and the Strength of Intermolecular Contact in Protein Crystals  

NASA Technical Reports Server (NTRS)

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

Matsuura, Yoshiki; Chernov, Alexander A.

2002-01-01

193

Noncovalent Interaction of Uridine 5?Monophosphate with Adenosine, Cytidine, and Thymidine, as well as Adenosine 5?Monophosphate and Cytidine 5?Monophosphate in Aqueous Solution  

Microsoft Academic Search

Adduct formation has been studied in the systems of uridine 5?-monophosphate (UMP) with adenosine (Ado), cytidine (Cyd), thymidine (Thd), adenosine 5?-monophosphate (AMP), and cytidine 5?-monophosphate (CMP) by the potentiometric method with computer analysis of the data and 13C and 31P NMR spectroscopic measurements. It has been established that in the complexes identified, ion–dipole and dipole–dipole interactions\\u000a occur with the positive

Lechoslaw Lomozik; Renata Jastrzab

2006-01-01

194

?-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

195

JOURNAL DE PHYSIQUE Colloque C2, supplPment au nO 3, Tome 40, mars 1979, page C2-363 MOSSBAUER SPECTROSCO?IC STUDIES OF THE INTERMOLECULAR INTERACTION  

E-print Network

in references /10,11/. The purity was checked by melting point, elemental analysis and assbauer parameters of intermolecular absolute value in the temperature dependence. We association and of molecular packing in a solid. The samples were obtained in polycrystalline powders and the "absolute" value and "celative" value

Paris-Sud XI, Université de

196

Desensitization and recovery of metastable intermolecular composites  

DOEpatents

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

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

2010-09-07

197

13C NMR reveals no evidence of n-?* interactions in proteins.  

PubMed

An n = ?* interaction between neighboring carbonyl groups has been postulated to stabilize protein structures. Such an interaction would affect the (13)C chemical shielding of the carbonyl groups, whose paramagnetic component is dominated by n = ?* and ? = ?* excitations. Model compound calculations indicate that both the interaction energetics and the chemical shielding of the carbonyl group are instead dominated by a classical dipole-dipole interaction. A set of high-resolution protein structures with associated carbonyl (13)C chemical shift assignments verifies this correlation and provides no evidence for an inter-carbonyl n = ?* interaction. PMID:22876300

Worley, Bradley; Richard, Georgia; Harbison, Gerard S; Powers, Robert

2012-01-01

198

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

SciTech Connect

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

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

2010-11-15

199

Rh-Catalyzed Intermolecular Reactions of Cyclic ?-Diazocarbonyl Compounds with Selectivity Over Tertiary C-H Bond Migration  

PubMed Central

Intermolecular Rh-catalyzed reactions of cyclic ?-diazocarbonyl compounds with chemoselectivity over ?-hydride elimination are described. These methods represent the first general intermolecular reactions of Rh-carbenoids that are selective over tertiary ?-C?H bond migration. Successful transformations include cyclopropanation, cyclopropenation, and various X–H insertion reactions with a broad scope of substrates. We propose that the intermolecular approach of substrates to carbenes from acyclic diazo precursors may be relatively slow due to a steric interaction with the ester function, which is perpendicular to the ?-system of the carbene. For carbenes derived from 5- and 6-membered cyclic ?-diazocarbonyls, it is proposed that the carbene is constrained to be more conjugated with the carbonyl, thereby relieving the steric interaction for intermolecular reactions, and accelerating the rate of intermolecular reactivity relative to intramolecular ?-hydride migration. However, attempts to use ?-diazo-?-ethylcaprolactone in intermolecular cyclopropanation with styrene were unsuccessful. It is proposed that the conformational flexibility of the 7-membered ring allows the carbonyl to be oriented perpendicular to Rh-carbene. The significant intermolecular interaction between the carbonyl and approaching substrate is in agreement with the poor ability of ?-diazo-?-ethylcaprolactone to participate in intermolecular cyclopropanation reactions. DFT calculations provide support for the mechanistic proposals that are described. PMID:22676258

DeAngelis, Andrew; Dmitrenko, Olga; Fox, Joseph M.

2012-01-01

200

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

NASA Astrophysics Data System (ADS)

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

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

2008-12-01

201

Kinetic theory for flows of nonhomogeneous rodlike liquid crystalline polymers with a nonlocal intermolecular potential.  

PubMed

The Doi kinetic theory for flows of homogeneous, rodlike liquid crystalline polymers (LCPs) is extended to model flows of nonhomogeneous, rodlike LCPs through a nonlocal (long-range) intermolecular potential. The theory features (i) a nonlocal, anisotropic, effective intermolecular potential in an integral form that is consistent with the chemical potential, (ii) short-range elasticity as well as long-range isotropic and anisotropic elasticity, (iii) a closed-form stress expression accounting for the nonlocal molecular interaction, and (iv) an extra elastic body force exclusively associated with the integral form of the intermolecular potential. With the effective intermolecular potential, the theory is proven to be well posed in that it warrants a positive entropy production and thereby the second law of thermodynamics. Approximate theories are obtained by gradient expansions of the number density function in the free energy density. PMID:12059561

Wang, Qi; E, Weinan; Liu, Chun; Zhang, Pingwen

2002-05-01

202

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

PubMed Central

The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O2 molecules interact predominantly through the half-filled 1?g* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1?g* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O2 molecules at the transition to the ?-phase. The ?-phase, which consists of (O2)4 clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O2)4 clusters develop upon compression of the ?-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases. PMID:18687889

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

2008-01-01

203

Tunable high-temperature thermodynamics of weakly interacting dipolar gases  

NASA Astrophysics Data System (ADS)

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

Daily, K. M.; Blume, D.

2014-01-01

204

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

PubMed

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

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

2011-10-01

205

Interactions between Rydberg-dressed atoms  

SciTech Connect

We examine interactions between atoms continuously and coherently driven between the ground state and a Rydberg state, producing 'Rydberg-dressed atoms'. Because of the large dipolar coupling between two Rydberg atoms, a small admixture of Rydberg character into a ground state can produce an atom with a dipole moment of a few debye, the appropriate size to observe interesting dipolar physics effects in cold atom systems. We have calculated the interaction energies for atoms that interact via the dipole-dipole interaction and find that because of blockade effects, the R dependent two-atom interaction terms are limited in size and can be R independent up until the dipolar energy is equal to the detuning. This produces R dependent interactions different from the expected 1/R{sup 3} dipolar form that have no direct analogy in condensed-matter physics and could lead to interesting quantum phases in trapped Rydberg systems.

Johnson, J. E.; Rolston, S. L. [Joint Quantum Institute, Department of Physics, University of Maryland (United States) and National Institute of Standards and Technology, College Park, Maryland 20742-4111 (United States)

2010-09-15

206

Hybrid materials from intermolecular associations between cationic lipid and polymers.  

PubMed

Intermolecular associations between a cationic lipid and two model polymers were evaluated from preparation and characterization of hybrid thin films cast on silicon wafers. The novel materials were prepared by spin-coating of a chloroformic solution of lipid and polymer on silicon wafer. Polymers tested for miscibility with the cationic lipid dioctadecyldimethylammonium bromide (DODAB) were polystyrene (PS) and poly(methyl methacrylate) (PMMA). The films thus obtained were characterized by ellipsometry, wettability, optical and atomic force microscopy, Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and activity against Escherichia coli. Whereas intermolecular ion-dipole interactions were available for the PMMA-DODAB interacting pair producing smooth PMMA-DODAB films, the absence of such interactions for PS-DODAB films caused lipid segregation, poor film stability (detachment from the silicon wafer) and large rugosity. In addition, the well-established but still remarkable antimicrobial DODAB properties were transferred to the novel hybrid PMMA/DODAB coating, which is demonstrated to be highly effective against E. coli. PMID:18630858

Pereira, Edla M A; Kosaka, Priscila M; Rosa, Heloísa; Vieira, Débora B; Kawano, Yoshio; Petri, Denise F S; Carmona-Ribeiro, Ana M

2008-08-01

207

Mapping intermolecular bonding in C60  

PubMed Central

The formation of intermolecular bonds in C60 has been investigated in detail at pressures below 2.2?GPa and up to 750?K. Fullerene samples were heated in a temperature gradient to obtain data on the formation of dimers and low-dimensional polymers along isobars. Intermolecular bonding was analyzed ex situ by Raman scattering, using both intramolecular modes and intermolecular stretching modes. Semi-quantitative reaction maps are given for the formation of dimers and chains. The activation energy for dimer formation decreases by 0.2?meV pm?1 when intermolecular distances decrease and dimer formation is noticeably affected by the rotational state of molecules. Above 400–450?K larger oligomers are formed; below 1.4?GPa most of these are disordered, with small domains of linear chains, but above this the appearance of stretching modes indicates the existence of ordered one-dimensional polymers. At the highest pressures and temperatures two-dimensional polymers are also observed. PMID:25145952

Sundqvist, Bertil

2014-01-01

208

Mapping intermolecular bonding in C60  

NASA Astrophysics Data System (ADS)

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

Sundqvist, Bertil

2014-08-01

209

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

NASA Technical Reports Server (NTRS)

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

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

1990-01-01

210

Thermodynamic curvature for attractive and repulsive intermolecular forces.  

PubMed

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

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

2013-09-01

211

Theory of Elastic Interaction of the Colloidal Particles in the Nematic Liquid Crystal Near One Wall and in the Nematic Cell  

E-print Network

We apply the method developed in Ref. [S.B.Chernyshuk and B.I.Lev, Phys.Rev.E, \\textbf{81}, 041701 (2010)] for theoretical investigation of colloidal elastic interactions between axially symmetric particles in the confined nematic liquid crystal (NLC) 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 \\textit{one} particle with the wall and within the nematic cell are found as well as corresponding \\textit{two particle} elastic interactions. A set of new 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 \\textit{isotropic attraction} is predicted for large distances $r>r_{dd}=4.76 h$; maps of attraction and repulsion zones are crucially changed for all interactions near the planar wall and in the planar cell; one dipole particle in the homeotropic nematic cell was found to be shifted by the distance $\\delta_{eq}$ from the center of the cell \\textit{independent} of the thickness $L$ 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 taken from [M.Vilfan et al. Phys.Rev.Lett. {\\bf 101}, 237801, (2008)] in the range $1\\div1000 kT$.

S. B. Chernyshuk; B. I. Lev

2011-01-10

212

n??* Interactions of Amides and Thioamides: Implications for Protein Stability  

PubMed Central

Carbonyl–carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n??* donor–acceptor interaction with an energy of at least 0.27 kcal/mol. The n??* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor–acceptor orbital interactions rather than dipole–dipole interactions. PMID:23663100

Newberry, Robert W.; VanVeller, Brett; Guzei, Ilia A.; Raines, Ronald T.

2013-01-01

213

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

PubMed

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

Boggs, J M

1987-10-01

214

Diastereoselective synthesis of tetrahydrofurans by Lewis acid catalyzed intermolecular carbenoid-carbonyl reaction-cycloaddition sequences: unusual diastereoselectivity of Lewis acid catalyzed cycloadditions.  

PubMed

The effects of including metal salts for three-component reactions involving ?-alkyl-?-diazo esters, aromatic aldehydes, and 3-(2-alkenoyl)-2-oxazolidinones are described, in terms of yields and diastereoselectivities. Metal tetrafluoroborates (10-30 mol %) such as Co(BF4)2·6H2O, Ni(BF4)2·6H2O, and AgBF4 were effective in delivering high yields and diastereoselectivities (93:7 to 99:1) of the corresponding tetrahydrofuran derivatives while suppressing the competitive formation of 1,3-dioxolane. Using (S)-3-(2-alkenoyl)-4-isopropyl-2-oxazolidinones as the dipolarophiles in the three-component reactions, in the presence of Ni(BF4)2·6H2O or Co(ClO4)2·6H2O (10-30 mol %), optically active tetrahydrofurans that possess four successive asymmetric centers were synthesized in high diastereoselectivities (99:1). On the basis of the configuration of the cycloadduct using the X-ray analysis, the high diastereoselectivity could be explained by the unusual Re-face approach to the dipolarophile in the presence of the Lewis acid, proceeding through the s-cis conformer of the 3-(2-alkenoyl)-2-oxazolidinone with the two carbonyls in opposing directions (dipole-dipole interaction). PMID:23758193

Hashimoto, Yuta; Itoh, Kennosuke; Kakehi, Akikazu; Shiro, Motoo; Suga, Hiroyuki

2013-06-21

215

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

216

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

217

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

NASA Astrophysics Data System (ADS)

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.

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

2014-04-01

218

Interpreting the widespread nonlinear force spectra of intermolecular bonds  

PubMed Central

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

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

2012-01-01

219

Interpreting the widespread nonlinear force spectra of intermolecular bonds.  

PubMed

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

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

2012-08-21

220

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

SciTech Connect

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

Ivchenko, I.N.

1985-07-01

221

Propagation studies of metastable intermolecular composites (MIC).  

SciTech Connect

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

Son, S. F. (Steven F.); Busse, J. R. (James R.); Asay, B. W. (Blaine W.); Peterson, P. D. (Paul D.); Mang, J. T. (Joseph T.); Bockmon, B. (Bryan); Pantoya, M. (Michelle)

2002-01-01

222

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.

223

Strongly interacting photons in hollow-core waveguides  

SciTech Connect

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

Shahmoon, Ephraim; Kurizki, Gershon [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel); Fleischhauer, Michael [Department of Physics and Research Center OPTIMAS, Technische Universitaet Kaiserslautern, DE-67663 Kaiserslautern (Germany); Petrosyan, David [Department of Physics and Research Center OPTIMAS, Technische Universitaet Kaiserslautern, DE-67663 Kaiserslautern (Germany); Institute of Electronic Structure and Laser, FORTH, GR-71110 Heraklion, Crete (Greece)

2011-03-15

224

Collision-induced absorption and anisotropy of the intermolecular potential  

NASA Astrophysics Data System (ADS)

A scheme is developed for quantum mechanical calculations of binary collision-induced spectra which permits full inclusion of rotovibrational molecular degrees of freedom. A close-coupling scheme which includes the radiation in the Hamiltonian is used. The collision- induced absorption spectra of interacting atom-diatom and diatom-diatom pairs are investigated. The inclusion of the anisotropy of the inter-molecular potential introduces couplings among the rotational levels of the diatomic molecules. Previous calculations of collision- induced spectra have almost exclusively been done using the isotropic potential approximation and we present an extensive investigation of the validity of that approximation. Absorption spectra in the rotational and fundamental bands of H 2, induced by collisions with He, H, Ar, and H2 are calculated for various temperatures. In all of these, except for H2- H, the anisotropy of the intermolecular potential affect the absorption by 5 10% in certain parts of the spectra. Comparisons with the available measurements show very good agreement of the shapes of the spectral profiles, although the absolute intensities differ by up to 10% in some cases. These remaining differences between theory and measurements appear to be random and are generally smaller than the differences among comparable measurements. In the H 2-H spectra the effect of the anisotropy of the potential turns out to be almost negligible at the temperature for which a full coupled quantum calculation was done. This is supported by spectral moment calculations. The smallness of the effect is believed to stern from the short range character of the anisotropy potential components for H2-H. Collision-induced absorption spectra of gaseous mixtures of deuterium hydride and helium in the rotational and fundamental bands of HD are calculated at a temperature of 77 K. The computed absorption profile agree with a measurement taken in the HD fundamental band. We also consider the interference phenomena of the HD permanent dipole with the HD-He interaction-induced dipole by computing the wings of various R(j) lines and of the P1(1) line in the single, binary collision limit. Agreement between theory and measurements is observed in the low-helium-density limit of the measured absorption line shapes.

Gustafsson, Magnus Sven

225

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

226

Proinsulin Intermolecular Interactions during Secretory Trafficking in Pancreatic ? Cells*  

PubMed Central

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

2013-01-01

227

AnEffective Approach for TeachingIntermolecularInteractions  

E-print Network

distribution of molecules. Organic chemistry speaks of electrophilic and nucleophilic re- agents, and certain reactions are explained with the aid of these concepts. In general, these concepts are based on the study

Campanario, Juan Miguel

228

Intermolecular constraints in the dynamics of semiflexible entangled polymer melts  

NASA Astrophysics Data System (ADS)

We present a Langevin equation for the contemporary dynamics of a group of interpenetrating semiflexible entangled polymer chains. The theory explicitly accounts for the intermolecular intermonomer repulsion between a pair of chains, generated by their inability to cross each other, i.e. the phenomenon of entanglements. The ``effective'' potential experienced by the chains arises from the repulsion between two monomers belonging to different chains, propagating through the chain connectivity, and the dynamics of chain interdiffusion and relaxation. With time the local hard-core potential is overcome by the relative motion of the polymers and the system relaxes. The same formalism applies to both unentangled and entangled melts. Short chains do not experience entanglements, because their relaxation process is faster than the average time that is necessary for the chain to diffuse a distance comparable to the mesh size, or length between two entanglements. Finally no a priori hypothesis has to be made about the processes that drive relaxation as the formalism is simply the conventional Rouse approach, generalized to treat the motion of interacting macromolecules, whose chains cannot cross each other.

Guenza, Marina

2012-02-01

229

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

NASA Astrophysics Data System (ADS)

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

Chaudhari, Sachin Rama; Suryaprakash, N.

2012-05-01

230

Modeling intermolecular effects on nonlinear optical properties of transition-metal complexes. An effective core potential study.  

PubMed

An initial effort to study the nonlinear optical (NLO) properties of interacting transition-metal-oxo complexes is presented and studied by effective core potential approaches. Osmium tetroxide is used for this study. Favorable intermolecular interaction effects, even within this weak interaction regime, that yield enhancements in NLO properties have been found. Interaction effects increase alpha (polarizability) up to 6% and gamma (second hyperpolarizability) up to 100% relative to the isolated monomer result for OsO4. The magnitude of the interaction (hyper)polarizabilities, and indeed even the sign, is found to be quite sensitive to the relative orientation of the osmium tetroxide monomers. PMID:11206380

Cundari, T R; Kurtz, H A; Zhou, T

2001-01-01

231

Optimization of Intermolecular Potential Parameters for the CO2/H2O Mixture.  

PubMed

Monte Carlo simulations in the Gibbs ensemble were used to obtain optimized intermolecular potential parameters to describe the phase behavior of the mixture CO2/H2O, over a range of temperatures and pressures relevant for carbon capture and sequestration processes. Commonly used fixed-point-charge force fields that include Lennard-Jones 12-6 (LJ) or exponential-6 (Exp-6) terms were used to describe CO2 and H2O intermolecular interactions. For force fields based on the LJ functional form, changes of the unlike interactions produced higher variations in the H2O-rich phase than in the CO2-rich phase. A major finding of the present study is that for these potentials, no combination of unlike interaction parameters is able to adequately represent properties of both phases. Changes to the partial charges of H2O were found to produce significant variations in both phases and are able to fit experimental data in both phases, at the cost of inaccuracies for the pure H2O properties. By contrast, for the Exp-6 case, optimization of a single parameter, the oxygen-oxygen unlike-pair interaction, was found sufficient to give accurate predictions of the solubilities in both phases while preserving accuracy in the pure component properties. These models are thus recommended for future molecular simulation studies of CO2/H2O mixtures. PMID:25198539

Orozco, Gustavo A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

2014-10-01

232

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

PubMed

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

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

2013-12-13

233

Anisotropic and long-range vortex interactions in two-dimensional dipolar Bose gases.  

PubMed

We perform a theoretical study into how dipole-dipole interactions modify the properties of superfluid vortices within the context of a two-dimensional atomic Bose gas of co-oriented dipoles. The reduced density at a vortex acts like a giant antidipole, changing the density profile and generating an effective dipolar potential centred at the vortex core whose most slowly decaying terms go as 1/?(2) and ln(?)/?(3). These effects modify the vortex-vortex interaction which, in particular, becomes anisotropic for dipoles polarized in the plane. Striking modifications to vortex-vortex dynamics are demonstrated, i.e., anisotropic corotation dynamics and the suppression of vortex annihilation. PMID:24206463

Mulkerin, B C; van Bijnen, R M W; O'Dell, D H J; Martin, A M; Parker, N G

2013-10-25

234

Protected State Enhanced Quantum Metrology with Interacting Two-Level Ensembles  

NASA Astrophysics Data System (ADS)

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

Ostermann, Laurin; Ritsch, Helmut; Genes, Claudiu

2013-09-01

235

Controlling the interactions of a few cold Rb Rydberg atoms by radiofrequency-assisted F\\"orster resonances  

E-print Network

Long-range interactions between cold Rydberg atoms are being investigated for neutral-atom quantum computing, quantum simulations, phase transitions in cold Rydberg gases and other important applications. These applications often require fine tuning of the interaction strength. It can be implemented using F\\"orster resonances between Rydberg atoms controlled by a dc, microwave or radiofrequency (rf) electric field. Here we report on the experimental observation of highly-resolved rf-assisted F\\"orster resonances in a few cold Rb Rydberg atoms. We also observed rf-induced F\\"orster resonances which cannot be tuned by dc electric field. They correspond to an efficient conversion between the van der Waals and dipole-dipole interactions due to Floquet sidebands of Rydberg levels appearing in the rf-field. These observations pave the way to many applications of rf-assisted F\\"orster resonances in studying the many-body phenomena with cold Rydberg atoms.

Tretyakov, D B; Yakshina, E A; Beterov, I I; Andreeva, Ch; Ryabtsev, I I

2014-01-01

236

Intra and intermolecular structure in the condensed phases of ethylene, ethane and carbon dioxide by neutron diffraction  

NASA Astrophysics Data System (ADS)

The distinct coherent scattering cross-sections for deuterated ethylene (C2D4) at 11·5 bar and 0·00911 mol Å-3, for deuterated ethane (C2D6) at 9·5 bar and 0·00996 mol Å-3 and for carbon dioxide (CO2) at 8·5 bar and 0·01597 mol Å-3 in their liquid phases have been obtained at 220K. These functions have been successfully separated into their intra and intermolecular contributions. The molecular structure of each liquid has been compared with the corresponding intramolecular configuration in both the solid and the gas phases. Intermolecular structure functions, im (Q), which contain information about intermolecular correlations, have been extracted. For CO2(l), the results have been compared with those obtained from molecular dynamic simulations and a reference interaction site model. The intermolecular potential proposed by Böhm et al. gives a good representation of CO2 liquid near the triple point. However orientational correlations between neighbouring molecules near the triple point, which disappear with increase of temperature, are not described by the model. The molecules in solid ethylene and ethane are packed loosely and the results show that there is only slight relaxation of the structure on melting. The correlation functions for ethylene and ethane have been compared with X-ray diffraction measurements analysed using scattering factors for -CH2 (in C2H4) and -CH3 (in C2H6) groups combined with different interaction models to obtain carbon-carbon intermolecular distribution functions.

Adya, Ashok K.; Wormald, Christopher J.

237

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

PubMed

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

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

2014-12-01

238

2-Dimensional Measurement of the Solvent Intermolecular Response in Solvation  

E-print Network

. The solvent intermolecular response in solvation is studied by 2-D polarizability response spectroscopy, reveal comparable translational vs. orientational dynamics. Although the collective chemical intuition- CH3CN system. See refs.3,4 for background. As shown in Fig. 1, 2-dimensional polarizability response

Scherer, Norbert F.

239

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

240

Dancing Crystals: A Dramatic Illustration of Intermolecular Forces  

ERIC Educational Resources Information Center

Crystals of naphthalene form on the surface of an acetone solution and dance about in an animated fashion illustrating surface tension, crystallization, and intermolecular forces. Additional experiments reveal the properties of the solution. Flows within the solutions can be visualized by various means. Previous demonstrations of surface motion…

Mundell, Donald W.

2007-01-01

241

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

NASA Astrophysics Data System (ADS)

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 (Cdbnd O and NH2) 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.

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

2012-09-01

242

Van der Waals interactions in density functional theory by combining the quantum harmonic oscillator-model with localized Wannier functions.  

PubMed

We present a new scheme to include the van der Waals (vdW) interactions in approximated Density Functional Theory (DFT) by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique. With respect to the recently developed DFT/vdW-WF2 method, also based on Wannier Functions, the new approach is more general, being no longer restricted to the case of well separated interacting fragments. Moreover, it includes higher than pairwise energy contributions, coming from the dipole-dipole coupling among quantum oscillators. The method is successfully applied to the popular S22 molecular database, and also to extended systems, namely graphite and H2 adsorbed on the Cu(111) metal surface (in this case metal screening effects are taken into account). The results are also compared with those obtained by other vdW-corrected DFT schemes. PMID:23927242

Silvestrelli, Pier Luigi

2013-08-01

243

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

PubMed

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

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

2012-01-01

244

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

245

From chaos to selective ordering of vortex cores in interacting mesomagnets  

NASA Astrophysics Data System (ADS)

A spin vortex consists of an in-plane curling magnetization and a small core region (~10?nm) with out-of-plane magnetization. An oscillating field or current induce gyrotropic precession of the spin vortex. Dipole-dipole and exchange coupling between the interacting vortices may lead to excitation of collective modes whose frequencies depend on the core polarities. Here we demonstrate an effective method for controlling the relative core polarities in a model system of overlapping Ni80Fe20 dots. This is achieved by driving the system to a chaotic regime of continuous core reversals and subsequently relaxing the cores to steady-state motion. It is shown that any particular core polarity combination (and therefore the spectral response of the entire system) can be deterministically preselected by tuning the excitation frequency or external magnetic field. We anticipate that this work would benefit the future development of magnonic crystals, spin-torque oscillators, magnetic storage and logic elements.

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

2012-12-01

246

Interaction effects on the magneto-optical response of magnetoplasmonic dimers  

NASA Astrophysics Data System (ADS)

The effect that dipole-dipole interactions have on the magneto-optical (MO) properties of magnetoplasmonic dimers is theoretically studied. The specific plasmonic versus magnetoplasmonic nature of the dimer's metallic components and their specific location within the dimer play a crucial role in the determination of these properties. We find that it is possible to generate an induced MO activity in a purely plasmonic component, even larger than that of the MO one, therefore dominating the overall MO spectral dependence of the system. Adequate stacking of these components may allow one to obtain, for specific spectral regions, larger MO activities in systems with a reduced amount of MO metal and therefore with lower optical losses. Theoretical results are contrasted and confirmed with experiments for selected structures.

de Sousa, N.; Froufe-Pérez, L. S.; Armelles, G.; Cebollada, A.; González, M. U.; García, F.; Meneses-Rodríguez, D.; García-Martín, A.

2014-05-01

247

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

248

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

PubMed

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

249

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

SciTech Connect

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

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

2011-06-30

250

Anisotropy in the Interactions of Ultracold Dysprosium  

NASA Astrophysics Data System (ADS)

The ground 4f^106s^2 configuration of atomic dysprosium has an unfilled 4f^10 shell lying beneath a closed 6s^2 shell. This so-called ``submerged-shell'' atom has a large orbital (L = 6) and total (J = 8) electron angular momenta and, consequently, an extremely large magnetic moment of 10?B. Only recently the first laser cooling and trapping experiment of dysprosium atoms has been reported [1]. The experiment suggested that the anisotropy from the submerged shell and magnetic moment plays a significant role in the interactions of dysprosium atoms. Here, we explore the anisotropies from the electrostatic dispersion and magnetic dipole-dipole interactions. We use a relativistic configuration interaction valence-bond method to obtain short-range chemical potentials. Dispersion coefficients have been calculated using known atomic data. Comparison of the strengths of dispersion and magnetic dipole interactions shows that the anisotropy in the dispersion dominates for atomic separations less than 50 bohr and can lead to a rapid reorientation of the Dy angular momenta.[4pt] [1] M. Lu, S. Ho Youn, and B. Lev, Phys. Rev. Lett. 104, 063001 (2010).

Kotochigova, Svetlana; Petrov, Alexander

2011-06-01

251

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

PubMed Central

A 1:2 mixture of [(S)-2](AuCl)2 [(S)-2 = (S)-3,5-t-Bu-4-MeO-MeOBIPHEP] and AgBF4 catalyzes the stereoconvergent, intermolecular enantioselective hydroamination of chiral, racemic 1,3-disubstituted allenes with N-unsubstituted carbamates to form N-allylic carbamates in good yield, with high regio- and diastereoselectivity, and up to 92% ee. PMID:22492591

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

2012-01-01

252

Bimorpholine-mediated enantioselective intramolecular and intermolecular aldol condensation.  

PubMed

Monosalts of N-substituted bimorpholine derivatives are efficient organocatalysts in intramolecular and intermolecular aldol reactions. The properties of the catalysts can be tuned either by the selection of an appropriate acid for the salt formation or by the change of a substituent at the nitrogen atom. In aldol condensation, i-Pr-substituted bimorpholine is the most stereoselective catalyst affording products in high yield with enantioselectivities up to 95% ee. PMID:17567073

Kanger, Tõnis; Kriis, Kadri; Laars, Marju; Kailas, Tiiu; Müürisepp, Aleksander-Mati; Pehk, Tõnis; Lopp, Margus

2007-07-01

253

Effect of spatial confinement on magnetic hyperthermia via dipolar interactions in Fe?O? nanoparticles for biomedical applications.  

PubMed

In this work, the effect of nanoparticle confinement on the magnetic relaxation of iron oxide (Fe3O4) nanoparticles (NP) was investigated by measuring the hyperthermia heating behavior in high frequency alternating magnetic field. Three different Fe3O4 nanoparticle systems having distinct nanoparticle configurations were studied in terms of magnetic hyperthermia heating rate and DC magnetization. All magnetic nanoparticle (MNP) systems were constructed using equivalent ~10nm diameter NP that were structured differently in terms of configuration, physical confinement, and interparticle spacing. The spatial confinement was achieved by embedding the Fe3O4 nanoparticles in the matrices of the polystyrene spheres of 100 nm, while the unconfined was the free Fe3O4 nanoparticles well-dispersed in the liquid via PAA surface coating. Assuming the identical core MNPs in each system, the heating behavior was analyzed in terms of particle freedom (or confinement), interparticle spacing, and magnetic coupling (or dipole-dipole interaction). DC magnetization data were correlated to the heating behavior with different material properties. Analysis of DC magnetization measurements showed deviation from classical Langevin behavior near saturation due to dipole interaction modification of the MNPs resulting in a high magnetic anisotropy. It was found that the Specific Absorption Rate (SAR) of the unconfined nanoparticle systems were significantly higher than those of confined (the MNPs embedded in the polystyrene matrix). This increase of SAR was found to be attributable to high Néel relaxation rate and hysteresis loss of the unconfined MNPs. It was also found that the dipole-dipole interactions can significantly reduce the global magnetic response of the MNPs and thereby decrease the SAR of the nanoparticle systems. PMID:25063092

Sadat, M E; Patel, Ronak; Sookoor, Jason; Bud'ko, Sergey L; Ewing, Rodney C; Zhang, Jiaming; Xu, Hong; Wang, Yilong; Pauletti, Giovanni M; Mast, David B; Shi, Donglu

2014-09-01

254

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

PubMed

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

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

2013-06-18

255

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

256

Intra- and intermolecular forces dependent main chain conformations of esters of ?,?-dehydroamino acids  

NASA Astrophysics Data System (ADS)

Esters of dehydroamino acids occur in nature. To investigate their conformational properties, the low-temperature structures of Ac-?Ala-OMe, Ac-?Val-OMe, Z-(Z)-?Abu-OMe, and Z-(Z)-?Abu-NHMe were studied by single-crystal X-ray diffraction. The ?Ala ester prefers the fully extended conformation C5. Both the ?Val and (Z)-?Abu esters assume the conformation ?, whereas the amide analogue of the latter prefers the conformation ?. For the conformations found, DFT calculations using B3LYP/6-311++G(d,p) with the SCRF-PCM and M062X/6-311++G(d,p) with the SCRF-SMD method were applied to mimicking chloroform and water environment. The tendency of the ?Val and (Z)-?Abu esters towards the conformation ?, and their amide analogues towards the conformation ?, with increase of the polarity of environment was found. The analysis of both intra- and intermolecular interactions including hydrogen bonds, carbonyl dipole attraction, and ?-electron conjugation, enabled to understand and elucidate the conformational preferences of studied compounds. The studies show how the molecular structure, and in consequence, the conformation adopted by molecules is influenced by the different intra- and intermolecular forces.

Siod?ak, Dawid; Bujak, Maciej; Sta?, Monika

2013-09-01

257

Pressure and temperature effects on intermolecular vibrational dynamics of ionic liquids  

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

258

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

259

Solute-solvent contact by intermolecular cross relaxation. I. The nature of the water-hydrophobic interface  

NASA Astrophysics Data System (ADS)

Intermolecular cross-relaxation rates between solute and solvent were measured by {1H} 19F nuclear magnetic resonance experiments in aqueous molecular solutions of ammonium perfluoro-octanoate and sodium trifluoroacetate. The experiments performed at three different magnetic fields provide frequency-dependent cross-relaxation rates which demonstrate clearly the lack of extreme narrowing for nuclear spin relaxation by diffusionally modulated intermolecular interactions. Supplemented by suitable intramolecular cross-relaxation, longitudinal relaxation, and self-diffusion data, the obtained cross-relaxation rates are evaluated within the framework of recent relaxation models and provide information about the hydrophobic hydration. In particular, water dynamics around the trifluoromethyl group in ammonium perfluoro-octanoate are more retarded than that in the smaller trifluoroacetate.

Nordstierna, Lars; Yushmanov, Pavel V.; Furó, István

2006-08-01

260

A unique quinolineboronic acid-based supramolecular structure that relies on double intermolecular B-N bonds for self-assembly in solid state and in solution  

PubMed Central

The boronic acid functional group plays very important roles in sugar recognition, catalysis, organic synthesis, and supramolecular assembly. Therefore, understanding the unique properties of this functional group is very important. 8-Quinolineboronic acid (8-QBA) is found to be capable of self-assembling in solid state through a unique intermolecular B-N bond mechanism reinforced by intermolecular boronic anhydride formation, ?-? stacking, and hydrogen bond formation. NMR NOE and diffusion studies indicate that intermolecular B-N interaction also exists in solution with 8-QBA. In contrast, a positional isomer of 8-QBA, 5-quinolineboronic acid (5-QBA) showed very different behaviors in crystal packing and in solution and therefore different supramolecular network. Understanding the structural features of this unique 8-QBA assembly could be very helpful for the future design of new sugar sensors, molecular catalysts, and supramolecular assemblies. PMID:18414645

Zhang, Yanling; Li, Minyong; Chandrasekaran, Sekar; Gao, Xingming; Fang, Xikui; Lee, Hsiau-Wei; Hardcastle, Kenneth; Yang, Jenny; Wang, Binghe

2007-01-01

261

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

262

Intermolecular Radical Carbofluorination of Non-activated Alkenes.  

PubMed

The Meerwein arylation has recently become an even more powerful tool for the functionalization of alkenes. Besides the attachment of an aryl group, radical reactions of this type allow the introduction of several different heteroatoms and a broad variety of alkenes are meanwhile tolerated as substrates. Closing a long-standing gap of the methodology, this communication describes the first intermolecular Meerwein-type carbofluorination. In metal-free reactions, arylalkyl fluorides were obtained from arylhydrazines and alkenes with Selectfluor acting as oxidant and as radical fluorine source. PMID:25303212

Kindt, Stephanie; Heinrich, Markus R

2014-11-17

263

Determination of stepsize parameters for intermolecular vibrational energy transfer  

SciTech Connect

The understanding of intermolecular vibrational energy transfer (IVET) is important since it is involved in any mechanism in which internal energy is added or removed from molecules. The database for the details of IVET for highly excited polyatomic molecules is inadequate and must be expanded. The overall objectives of this project are: (1) to determine the dependence of energy relaxation on excitation energy and on the molecular complexity of substrate and deactivator, (2) to assess the importance of intermolecular attractions on IVET, (3) to obtain more detailed information on the energy distribution after collision, and (4) to evaluate the importance of IVET on high temperature unimolecular reactions. The first three objectives are being met by experimentally measuring the time evolution of the average energy of the vibrationally excited species (hydro- and fluoro- carbons excited by a pulsed CO{sub 2} laser) and the average energy transferred into relative translation via time resolved IR spectrometry, interferometry and optoacoustic techniques. Trajectory calculations simulating IVET are being performed for model substrate/deactivator pairs to provide additional details and insight on the critical parameters. Our calculations for high temperature unimolecular reactions indicate that IVET effects are significant and must be correctly taken into account. 9 refs., 3 figs., 6 tabs.

Tardy, D.C.

1989-06-01

264

On the theory of double quantum NMR in polymer systems: The second cumulant approximation for many spin I = 1/2 systems  

SciTech Connect

General analytical expressions for Double Quantum Nuclear Magnetic Resonance (DQ NMR) kinetic curves of many-spin I = 1/2 systems are derived with an accuracy of the second cumulant approximation. The expressions obtained exactly describe the initial part of the kinetic curves and provide a reasonable approximation up to times of about the effective spin-relaxation time. For the case when the system contains two isolated spins, this result exactly reproduces known expressions. In the case of polymer melts, the intermolecular magnetic dipole-dipole interactions significantly influence the time dependence of the DQ NMR kinetic curves.

Fatkullin, N. [Institute of Physics, Kazan Federal University, Kazan, 420008 Tatarstan (Russian Federation)] [Institute of Physics, Kazan Federal University, Kazan, 420008 Tatarstan (Russian Federation); Mattea, C.; Stapf, S. [Dept. Technical Physics II, Technische Universität Ilmenau, 98684 Ilmenau (Germany)] [Dept. Technical Physics II, Technische Universität Ilmenau, 98684 Ilmenau (Germany)

2013-11-21

265

Transetherification on polyols by intra- and intermolecular nucleophilic substitutions.  

PubMed

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

266

Intermolecular hydrogen-bonded organic semiconductors—Quinacridone versus pentacene  

NASA Astrophysics Data System (ADS)

Quinacridone is a five-ring hydrogen-bonded molecule analogous in structure and size to the well-known organic semiconductor pentacene. Unlike pentacene, quinacridone has limited intramolecular ?-conjugation and becomes highly colored in the solid state due to strong intermolecular electronic coupling. We found that quinacridone shows a field-effect mobility of 0.1 cm2/V.s, comparable to mobilities of pentacene in similarly prepared devices. Photoinduced charge generation in single-layer quinacridone metal-insulator-metal diodes is more than a hundred times more efficient than in pentacene devices. Photoinduced charge transfer from quinacridone to C60 is not effective, as evidenced by measurements in heterojunctions with C60. Hydrogen-bonded organic solids may provide new avenues for organic semiconductor design.

Daniel G?owacki, Eric; Leonat, Lucia; Irimia-Vladu, Mihai; Schwödiauer, Reinhard; Ullah, Mujeeb; Sitter, Helmut; Bauer, Siegfried; Serdar Sariciftci, Niyazi

2012-07-01

267

Substituent effects on intermolecular .hydrogen bonding from a lattice gas theory for lower critical solution points  

E-print Network

Substituent effects on intermolecular .hydrogen bonding from a lattice gas theory for lower transitions in binary mixtures with hydrogen bonding, introduced and studied by Walker, Vause, and Goldstein of the intermolecular hydrogen bonding. The parametric trends are found to agree with those expected from consideration

Goldstein, Raymond E.

268

Isothermal volume derivative of thermodynamic Gruneisen parameter, nonlinearity parameter and intermolecular heat capacity of liquids  

Microsoft Academic Search

The isochoric temperature derivative of Sound Velocity, the isothermal volume derivative of thermodynamic Gruneisen parameter, fractional free (available) volume and the repulsive exponent of intermolecular potential are shown to be related to t he microscopic Gruneisen parameter and Beyer's nonlinearity parameter of the liquid, The intermolecular contributions to the heat capacity and the adiabatic bulk modulw have been evaluated from

B. K. SHARMA

1994-01-01

269

Meeting the challenge of intermolecular gold(i)-catalyzed cycloadditions of alkynes and allenes.  

PubMed

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

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

2014-11-01

270

DOI: 10.1002/cphc.200700504 Static and Frequency-Dependent DipoleDipole  

E-print Network

. The reference static electric dipole polarizability of palladium has been obtained by finite- field calculations degrades when considering the full set of atoms. In general, we find that conclusions based on results region. [a] Dr. R. Bast, Dr. T. Saue Institut de Chimie UMR 7177 CNRS/UniversitÃ? Louis Pasteur Lab

Helgaker, Trygve

271

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

PubMed Central

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

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

2013-01-01

272

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

273

Scaling of the Local Dynamics and the Intermolecular Potential  

E-print Network

The experimental fact that relaxation times, tau, of supercooled liquids and polymers are uniquely defined by the quantity TV^g, where T is temperature, V specific volume, and g a material constant, leads to a number of interpretations and predictions concerning the dynamics of vitrification. Herein we examine means to determine the scaling exponent g apart from the usual superpositioning of relaxation data. If the intermolecular potential can be approximated by an inverse power law, as implied by the TV^g scaling, various equations are derived relating g to the Gruneisen parameter and to a common expression for the pressure derivative of the glass temperature. In addition, without assumptions, g can be obtained directly from pressure-volume-temperature data. These methods for determining g from molecular or thermodynamic properties are useful because they enable the P- and V-dependences of tau to be obtained, and thereby various analyses of the dynamics to be explored, without the need to carry out relaxation measurements beyond ambient pressure.

C. M. Roland; J. L. Feldman; R. Casalini

2006-02-06

274

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

275

Intermolecular vibrational energy exchange directly probed with ultrafast two dimensional infrared spectroscopy  

NASA Astrophysics Data System (ADS)

Ultrafast two dimensional infrared (2D IR) spectroscopy has been applied to probe the intermolecular vibrational energy exchange between two model molecules, benzonitrile and acetonitrile-d3. The vibrational energy exchange between these two molecules is manifested through the growth of cross peaks in their 2D IR spectra. In experiments, their nitrile groups (CN) are not involved in the energy exchange but serve as reporters of the process. Our experiments demonstrate that intermolecular vibrational energy transfer can be directly probed with the 2D IR method. Results also show that the mode specific energy transfer can be important in intermolecular vibrational energy transfers.

Bian, Hongtao; Zhao, Wei; Zheng, Junrong

2009-09-01

276

Theoretical study of the Ar-, Kr-, and Xe-CH4, -CF4 intermolecular potential-energy surfaces.  

PubMed

We present a theoretical study of the intermolecular potentials for the Ar, Kr, and Xe-CH4, -CF4 systems. The potential-energy surfaces of these systems have been calculated utilizing second-order Möller-Plesset perturbation theory and coupled-cluster theory in combination with correlation-consistent basis sets (aug-cc-pvnz; n = d, t, q). The calculations show that the stabilizing interactions between the rare gases and the molecules are slightly larger for CF4 than for CH4. Moreover, the rare-gas-CX4 (X = H, F) potentials are more attractive for Xe than for Kr and Ar. Our highest quality ab initio data (focal-point-CCSD(T) extrapolated to the complete basis set limit) have been used to develop pairwise analytical potentials for rare-gas-hydrocarbon (-fluorocarbon) systems. These potentials can be applied in classical-trajectory studies of rare gases interacting with hydrocarbon surfaces. PMID:16970379

Alexander, William A; Troya, Diego

2006-09-21

277

Parameterization of a B3LYP specific correction for non-covalent interactions and basis set superposition error on a gigantic dataset of CCSD(T) quality non-covalent interaction energies  

PubMed Central

A vast number of non-covalent interaction energies at the counterpoise corrected CCSD(T) level have been collected from the literature to build a diverse new dataset. The whole dataset, which consists of 2027 CCSD(T) energies, includes most of the published data at this level. A large subset of the data was then used to train a novel, B3LYP specific, empirical correction scheme for non-covalent interactions and basis set superposition error (abbreviated as B3LYP-MM). Results obtained with our new correction scheme were directly compared to benchmark results obtained with B3LYP-D31 and M06-2X2 (two popular density functions designed specifically to accurately model non-covalent interactions). For non-covalent complexes dominated by dispersion or dipole-dipole interactions all three tested methods give accurate results with the medium size aug-cc-pVDZ3–6 basis set with MUE’s of 0.27 (B3LYP-MM), 0.32 (B3LYP-D3) and 0.47 kcal/mol (M06-2X) (with explicit counterpoise corrections). These results validate both B3LYP-D3 and M06-2X for interactions of this type using a much larger data set than was presented in prior work. However, our new dispersion correction scheme shows some clear advantages for dispersion and dipole-dipole dominated complexes with the small LACVP* basis set, which is very popular in use due to its low associated computational cost: The MUE for B3LYP-MM with the LACVP* basis set for this subset of complexes (without explicit counterpoise corrections) is only 0.28 kcal/mol, compared to 0.65 kcal/mol for M06-2X or 1.16 kcal/mol for B3LYP-D3. Additionally, our new correction scheme also shows major improvements in accuracy for hydrogen-bonded systems and for systems involving ionic interactions, for example cation-? interactions. Compared to B3LYP-D3 and M06-2X, we also find that our new B3LYP-MM correction scheme gives results of higher or equal accuracy for a large dataset of conformer energies of di- and tripeptides, sugars, and cysteine. PMID:22058661

Schneebeli, Severin T.; Bochevarov, Arteum D.; Friesner, Richard A.

2011-01-01

278

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

279

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

PubMed

Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies. PMID:25362343

Yusufaly, Tahir I; Li, Yun; Singh, Gautam; Olson, Wilma K

2014-10-28

280

Arginine-phosphate salt bridges between histones and DNA: Intermolecular actuators that control nucleosome architecture  

NASA Astrophysics Data System (ADS)

Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies.

Yusufaly, Tahir I.; Li, Yun; Singh, Gautam; Olson, Wilma K.

2014-10-01

281

Anisotropy mapping in rat brains using Intermolecular Multiple Quantum Coherence Effects  

E-print Network

This document reports an unconventional and rapidly developing approach to magnetic resonance imaging (MRI) using intermolecular multiple-quantum coherences (iMQCs). Rat brain images are acquired using iMQCs. We detect iMQCs between spins that are 10 {\\mu}m to 500 {\\mu}m apart. The interaction between spins is dependent on different directions. We can choose the directions on physical Z, Y and X axis by choosing correlation gradients along those directions. As an important application, iMQCs can be used for anisotropy mapping. In the rat brains, we investigate tissue microstructure. We simulated images expected from rat brains without microstructure. We compare those with experimental results to prove that the dipolar field from the overall shape only has small contributions to the experimental iMQC signal. Because of the underlying low signal to noise ratio (SNR) in iMQCs, this anisotropy mapping method still has comparatively large potentials to grow. The ultimate goal of my project is to develop creative a...

Han, Yi

2014-01-01

282

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

283

Self-assembly of NH-pyrazoles via intermolecular N-H.N hydrogen bonds.  

PubMed

The crystal structures of two NH-pyrazole derivatives forming intermolecular N-H.N hydrogen bonds are reported: 5-methyl-4-(3-methylpyrazol-5-yl)pyrazol-3-ol, C(8)H(10)N(4)O (P1), and 3-methyl-5-dihydro-1H-naphtho[1,2-d]pyrazole hemihydrochloride, C(12)H(12)N(2).-C(12)H(13)N(2)(+).Cl(-) (P2). 26 other structures are surveyed in order to obtain a deeper insight into the ways NH-pyrazoles self-assemble by means of intermolecular N-H.N hydrogen bonds in molecular crystals. A limited number of compounds form chains or dimers via homonuclear N(+)-H.N positive-charge-assisted hydrogen bonds, typical of proton sponges, which can be remarkably short [e.g. N.N 2.714 (3), N-H 1.09 (3), H.N 1.63 (3) Å, N-H.N 169 (3) degrees in (P2)]. Most pyrazoles, however, pack via neutral N-H.N bonds which are formally assisted by resonance (resonance-assisted hydrogen bond, RAHB) through the.N=C-C=C-NH. iminoenamine fragment, contained in the ring, giving rise to dimers, trimers, tetramers and infinite chains of pyrazole molecules. Surprisingly, the resonance does not appear to shorten the N-H.N bond with respect to the accepted mean value N.N 2.97 (10) Å for non-resonant N-H.N bonds. It is shown that this is due to the internal pi-delocalization of the pyrazole ring, which can be hardly increased by the hydrogen-bond interaction, except in symmetrically 3,5-substituted pyrazoles which display N.N distances as short as 2.82 Å, identical C-C and C-N distances in the two halves of the pyrazole molecule, and typical phenomena of N-H.N dynamical proton disorder, detectable by (15)N-CP/MAS solid-state NMR. PMID:10927441

Bertolasi; Gilli; Ferretti; Gilli; Fernàndez-Castaño

1999-12-01

284

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

285

Fast acquisition of high-resolution NMR spectra in inhomogeneous fields via intermolecular double-quantum coherences  

PubMed Central

A pulse sequence, IDEAL-II, is proposed based on the concept of intermolecular dipolar-interaction enhanced all lines [Z. Chen et al., J. Am. Chem. Soc. 126, 446 (2004)] for obtaining one-dimensional (1D) high-resolution liquid NMR spectra in inhomogeneous fields via two-dimensional acquisitions. With the new acquisition scheme, the range of magnetic field inhomogeneity rather than chemical shift is sampled in the indirect dimension. This enables a great reduction in acquisition time and amount of data, much improved over the original IDEAL implementation. It is applicable to both isolated and J-coupled spin systems in liquid. For the latter, apparent J coupling constants are magnified threefold in spectra obtained with this sequence. This allows a more accurate measurement of J coupling constants in the cases of small J coupling constants or large inhomogeneous fields. Analytical expression was derived based on intermolecular multiple-quantum coherence treatments. Solution samples that were purposely deshimmed and biological samples with intrinsic field inhomogeneities were tested. Experimental results demonstrate that this sequence retains useful structural information including chemical shifts, relative peak areas, and multiplet patterns of J coupling even when the field inhomogeneity is severe enough to almost erase all spectroscopic information with conventional 1D single-quantum coherence techniques. This sequence is more applicable to weakly coupled and uncoupled spin systems, potentially useful for studying metabolites in in vivo NMR spectroscopy and for characterizing technologically important new materials in combinatorial chemistry. PMID:19256612

Chen, Zhong; Cai, Shuhui; Chen, Zhiwei; Zhong, Jianhui

2009-01-01

286

Spectral Moments of Collision-Induced Absorption of CO2 Pairs: The Role of the Intermolecular Potential  

NASA Technical Reports Server (NTRS)

In this paper we examine the role of the anisotropy of the intermolecular potential in the rototranslational collision-induced absorption of the CO2 pairs. Using newly developed formulas that include the effects of anisotropy of the potential to all orders, we calculate the two lowest spectral moments gamma(prime), and alpha(prime), for four different classes of C02 pair potentials and compare the results with the experimental values. We assumed only multipolar induction in the process of forming the induced dipole, with the second-order contributions included. Using a site-site LJ and a site-site semi-ab initio intermolecular potentials we were able to reproduce the experimental values of gamma(prime), and alpha(prime) moments over entire temperature range from 230 to 330 K. Also, the role of an electrostatic interaction between two C02 molecules and its impact on the spectral moments is thoroughly investigated. An isotropic core with a point quadrupole centered at each molecule is shown to be an inadequate representation of the C02-CO2 potential. Additionally, we show the results obtained with the first- and second-order perturbation theory to be more than twice too small.

Gruszka, Marcin; Borysow, Aleksandra

1994-01-01

287

Fast acquisition of high-resolution NMR spectra in inhomogeneous fields via intermolecular double-quantum coherences  

NASA Astrophysics Data System (ADS)

A pulse sequence, IDEAL-II, is proposed based on the concept of intermolecular dipolar-interaction enhanced all lines [Z. Chen et al., J. Am. Chem. Soc. 126, 446 (2004)] for obtaining one-dimensional (1D) high-resolution liquid NMR spectra in inhomogeneous fields via two-dimensional acquisitions. With the new acquisition scheme, the range of magnetic field inhomogeneity rather than chemical shift is sampled in the indirect dimension. This enables a great reduction in acquisition time and amount of data, much improved over the original IDEAL implementation. It is applicable to both isolated and J-coupled spin systems in liquid. For the latter, apparent J coupling constants are magnified threefold in spectra obtained with this sequence. This allows a more accurate measurement of J coupling constants in the cases of small J coupling constants or large inhomogeneous fields. Analytical expression was derived based on intermolecular multiple-quantum coherence treatments. Solution samples that were purposely deshimmed and biological samples with intrinsic field inhomogeneities were tested. Experimental results demonstrate that this sequence retains useful structural information including chemical shifts, relative peak areas, and multiplet patterns of J coupling even when the field inhomogeneity is severe enough to almost erase all spectroscopic information with conventional 1D single-quantum coherence techniques. This sequence is more applicable to weakly coupled and uncoupled spin systems, potentially useful for studying metabolites in in vivo NMR spectroscopy and for characterizing technologically important new materials in combinatorial chemistry.

Chen, Zhong; Cai, Shuhui; Chen, Zhiwei; Zhong, Jianhui

2009-02-01

288

Single-molecule studies of DNA dynamics and intermolecular forces  

NASA Astrophysics Data System (ADS)

DNA molecules were used as a model system to investigate fundamental problems in polymer physics; namely, how molecular length, topology and concentration influence the dynamical properties of polymers. A set of DNA molecules suitable for polymer studies was prepared using molecular biology techniques. Video fluorescence microscopy and single-molecule tracking were used to determine self-diffusion coefficients of DNA molecules. Optical tweezers were used to measure the intermolecular forces confining entangled DNA molecules. Scaling of diffusion with molecular length was in agreement with the Zimm model for dilute solutions of linear and circular DNA, indicating that excluded volume effects are appreciable for both topologies. Scaling of diffusion with concentration was also determined for the four possible topological combinations of linear and circular molecules: linear DNA diffusing in a solution of linear DNA, linear DNA in circular DNA, circular in circular, and circular in linear. For lower concentrations molecular topology had little effect and scaling was in agreement with that of the Rouse model. As concentration was increased topology played a much larger role and scaling crossed over to that of the reptation model, predicted to describe the dynamics of entangled polymers. The notable exception was the strongly hindered diffusion observed for a circular molecule diffusing in an entangled linear solution, suggesting the importance of constraint release. Using a new experimental approach with optical tweezers, a tube-like field confining a single entangled molecule was measured, in accord with the key assumption of the reptation model. A time-dependent harmonic potential opposed displacement transverse to the molecular contour, and the force relaxations following displacement were composed of three distinct modes. A characteristic tube radius of the entangled solution was also determined, close to the classically predicted value. The dependence of the above findings on molecular topology and concentration was also investigated. In particular, for an entangled solution of circular DNA of the same length and concentration, the confining tube radius was 25% smaller and the longest relaxation time was ˜3 times shorter than with linear DNA. For large displacements the confining force for circular DNA was also substantially lower and shorter range than that measured with linear DNA.

Robertson, Rae Marie

289

[Study of interaction of umbelliferone with three aromatic amino acids by fluorescence spectroscopy].  

PubMed

The interaction between umbelliferone (UMB) with tryptophan (Trp), tyrosine (Tyr) and phenylalanine (Phe) was studied by using fluorescence (FS) and ultraviolet (UV) spectroscopy. The results show that UMB can strongly quench the fluorescence of the three aromatic amino acids with the maximum quenching wavelengths at 347, 303 and 282 nm, respectively. Data analyses based on the Stern-Volmer curve and the UV spectroscopy show that static quenching occurred through the formation of the complexes of UMB with each aromatic amino acid in a molar ratio of 1 : 1. The binding constant K(c) of UMB with Trp, Tyr and Phe is 2.993 x 10(6), 7.858 x 10(4) and 1.186 x 10(3) L x mol(-1) (298.15 K) and 2.702 x 10(4), 1.063 x 10(5) and 8.352 x 10(3) L x mol(-1) (310.15 K), respectively. The thermodynamic parameters indicate that UMB has a strong interaction with the three aromatic amino acids. Hydrogen bond and Van der Waals force may play a major role in the reaction of UMB with Trp, whereas hydrophobic interaction should be responsible for the binding of UMB with Tyr and Phe. In addition, the dipole-dipole interaction may be another factor in the reactions between UMB and the three aromatic aminoacids. PMID:24159859

Jiang, Huan; Zhu, Yan-Wu; Wang, Yan; He, Jian-Bo

2013-08-01

290

Direct determination of weak exchange interactions in Cr3+-doped spinel ZnGa2O4  

NASA Astrophysics Data System (ADS)

Low-temperature electron-spin-resonance spectra of Cr3+-doped ZnGa2O4 exhibit numerous weak lines, which are due to isolated non-nearest-neighbor Cr3+-Cr3+ pairs. From an analysis of these spectra it is possible to determine the magnetic exchange interactions up to the sixth-neighbor shell. The assignment of the lines to definite types of pairs is facilitated by using the strain-modulation technique. If the interaction is written as Hex=-JiS-->0.S-->i+Han the exchange constants Ji are found to be: J2=-0.94 cm-1, J3=-1.22 cm-1, J4=-0.80 cm-1, J5=-0.45 cm-1, and J6=-0.55 cm-1. The error margin is +/-0.01 cm-1 in all cases. The anisotropic part of the interaction Han can be fully accounted for by magnetic dipole-dipole interaction. The results are discussed in terms of a simple exchange-path model. It turns out that anion-anion interaction is comparable in strength with anion-cation interaction. Using the above-given set of Ji values, together with the previously determined value of J1=-22.2+/-0.5 cm-1, it is possible to reproduce the asymptotic Curie temperature of ZnCr2O4 to within an accuracy of 10%.

Henning, J. C. M.

1980-06-01

291

Unconventional diffusion behaviors of intermolecular multiple-quantum coherences in nuclear magnetic resonance  

NASA Astrophysics Data System (ADS)

To date, both the intermolecular multiple-quantum coherence (MQC) and demagnetizing field models have led to fully quantitative predictions of NMR signals in a highly polarized system using the CRAZED and similar sequences. In this paper, measurements of apparent MQC diffusion rates, Dnapp, for a specific apparent coherence order, n, were used to investigate the equivalent between the intermolecular MQC and demagnetizing field treatments. A number of physical effects were analyzed both theoretically and experimentally. These effects include molecular diffusion, variation in dipolar correlation distance, radiation damping, inhomogeneous broadening, and spin relaxation, all of which may alter the NMR signal. Two variations of a two-pulse CRAZED sequence, where the signal attenuation is almost entirely caused by the diffusion weighting, were designed to accurately measure and characterize Dnapp during the evolution period. Apparent diffusion rates were extracted from a least-squares fitting of a series of 1H spectra, measured with varying diffusion weighting factors. Complete theoretical formations were explicitly derived from both the intermolecular MQC and demagnetizing field treatments. Numerical simulations based on the demagnetizing field treatment were performed and it was found that the model can be used to predict the apparent diffusion rates. A novel diffusion model for intermolecular MQC is proposed in which the phase shift of each individual spin on different molecules is considered to be uncorrelated. This model successfully predicts the unconventional diffusion behaviors of intermolecular MQCs, specifically for differences of apparent diffusion rates between inter- and intramolecular MQCs. Our theoretical predictions and experimental confirmation demonstrate, for the first time, that Dnapp for intermolecular MQCs of order n are characterized by Dnapp=nDT for n?2 and D0app=2DT for n=0, where DT is the translational molecular diffusion rate of the single quantum coherences. These results do not coincide with Dn=n2DT for n?0 which is a general relationship for an intramolecular n-quantum coherence. These works about the apparent diffusion rates during the evolution period of the CRAZED sequences provide additional evidence to support the argument of the equivalence between the intermolecular MQC and demagnetizing field models. The general results derived from both intermolecular MQC and demagnetizing field treatments in this report can reasonably explain new observations of diffusion phenomena in nonlinear spin echoes by Kimmich and co-workers. Even though the theoretical prediction about intermolecular MQC diffusion is verified only with specific experiments using tailor-made pulse sequences, it is demonstrated that the function dependence of diffusion rate on coherence order is general. These results provide independent evidence to support the intermolecular MQC theory proposed by Warren and co-workers.

Chen, Zhong; Zhong, Jianhui

2001-04-01

292

Studies of low-frequency intermolecular hydrogen-bonded vibrations using a continuous supersonic slit jet mid-infrared quantum cascade laser spectrometer  

NASA Astrophysics Data System (ADS)

Rovibrational manifolds in low frequency intermolecular vibrations of prototypical hydrogen-bonded interactions OC-HX (X = F, Cl, CN) are reported using a near infrared quantum cascade cw supersonic jet spectrometer. (i) OC-HCl is studied to evaluate future capabilities of the QCL spectrometer. (ii) Analysis of OC-HF demonstrates applicability to vibrations greater than 80 cm-1 above the ground state. ?51 band origins in OC-1H35Cl and OC-1H19F are 48.9944(2) and 81.96825(12) cm-1 respectively. (iii) The corresponding intermolecular ?71 band origin of OC-HCN is 34.63742(18) cm-1 and its corresponding rovibrational spectrum made available for attempted detection in interstellar space. Analysis of ?2, ?2+?71-?71, ?2+?71, and ?2+?61 vibrations in OC-HCN also enables generation of its 5-dimensional semi-empirical intermolecular potential. Structural and other properties of OC-HCN are then compared with corresponding properties predicted using morphed potentials for the homologous series OC-HX (X = F, Cl, Br, I). These results permit investigation of blue shifts in OC vibrations for this homologous series.

McElmurry, B. A.; Rivera-Rivera, L. A.; Scott, K. W.; Wang, Z.; Leonov, I. I.; Lucchese, R. R.; Bevan, J. W.

2012-12-01

293

Intermolecular momentum transfer in poly(perfluorosulfonic acid) membrane hydrated by aqueous solution of methanol: A molecular dynamics simulation study  

NASA Astrophysics Data System (ADS)

Intermolecular momentum transfer in methanol-water mixture solvated poly(perfluoro-sulfonic acid) membrane is studied in terms of center of mass velocity cross-correlation functions between molecular mass centers in their first coordination shells based on molecular dynamics simulations. Moreover, the center of mass velocity cross-correlation functions are also decomposed into longitudinal and transversal contributions. The fastest momentum transfer is observed between hydronium cation and water molecule due to the strong hydrogen bond interaction. The center of mass velocity cross-correlation functions reach peak value in about 36 fs, corresponding to a single collision with a neighboring molecule. For the momentum transfer between the water molecule and methanol molecule, the peaking time is 70 fs or about twice of that between hydronium cation and water molecule. Oscillation of the center of mass velocity cross-correlation functions between hydronium cation and water molecule is also observed due to the cage effect in their equilibrium positions.

Shao, Changle; Yan, Liuming; Ji, Xiaobo; Zhu, Suhua

2009-12-01

294

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

295

Intermolecular Casimir-Polder Forces in Water and near Surfaces  

E-print Network

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; Sernelius, Bo E; Parsons, Drew F; Malthe-Sørenssen, Anders; Boström, Mathias

2014-01-01

296

van der Waals interaction in excited alkali-metal dimers  

NASA Astrophysics Data System (ADS)

We have studied the long-range interaction potentials of the heteronuclear alkali-metal-atom dimers in the case when one of the atoms is in the first excited state (nAP) and the other is in the ground state (nBS). The presentation of the general expressions for the interaction energies in the Hund's case (c) is followed by the calculation of the corresponding C6 constants for all heteronuclear alkali-metal-atom pairs. In the case of heavier perturbers (Rb and Cs) the C6 constants are found to be significantly influenced by the perturber's fine structure. The van der Waals interaction in the K-Rb system is exceptionally strong resulting in C6 constants considerably larger than in all other alkali-metal-atom heteronuclear systems. The intermediate-coupling region (ICR) is defined as the region of internuclear separation R where the interaction energy is of the order of the atomic spin-orbit splitting, while the exchange energy is still negligible. Analysis of the general form of the energy matrices in the ICR shows that the homonuclear alkali-metal-atom dimers can be treated as a special case. In the large-R limit, the ICR results reduce to those obtained in Hund's case (c). As an example, we have calculated the ICR interaction potentials of the K-Rb system, taking into account only the leading dipole-dipole interaction. Finally we have discussed the construction of the absorption coefficient in the wings of the resonance lines, both in the impact and in the quasistatic approximation.

Movre, Mladen; Beuc, Robert

1985-05-01

297

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

298

Multiple-scattering approach to interatomic interactions and superradiance in inhomogeneous dielectrics  

SciTech Connect

The dynamics of a collection of resonant atoms embedded inside an inhomogeneous nondispersive and lossless dielectric is described with a dipole Hamiltonian that is based on a canonical quantization theory. The dielectric is described macroscopically by a position-dependent dielectric function and the atoms as microscopic harmonic oscillators. We identify and discuss the role of several types of Green tensors that describe the spatio-temporal propagation of field operators. After integrating out the atomic degrees of freedom, a multiple-scattering formalism emerges in which an exact Lippmann-Schwinger equation for the electric field operator plays a central role. The equation describes atoms as point sources and point scatterers for light. First, single-atom properties are calculated such as position-dependent spontaneous-emission rates as well as differential cross sections for elastic scattering and for resonance fluorescence. Secondly, multiatom processes are studied. It is shown that the medium modifies both the resonant and the static parts of the dipole-dipole interactions. These interatomic interactions may cause the atoms to scatter and emit light cooperatively. Unlike in free space, differences in position-dependent emission rates and radiative line shifts influence cooperative decay in the dielectric. As a generic example, it is shown that near a partially reflecting plane there is a sharp transition from two-atom superradiance to single-atom emission as the atomic positions are varied.

Wubs, Martijn [Complex Photonic Systems, Faculty of Science and Technology, University of Twente, P.O. Box 217, NL-7500 AE Enschede (Netherlands); Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, NL-1018 XE Amsterdam (Netherlands); Suttorp, L.G. [Institute for Theoretical Physics, University of Amsterdam, Valckenierstraat 65, NL-1018 XE Amsterdam (Netherlands); Lagendijk, A. [Complex Photonic Systems, Faculty of Science and Technology, University of Twente, P.O. Box 217, NL-7500 AE Enschede (Netherlands)

2004-11-01

299

Memory Effects and Inter-particle Interactions in Co Nanoparticles Embedded in Carbon Matrix  

NASA Astrophysics Data System (ADS)

In this work we have studied the magnetic properties of face-centered-cubic (fcc) Co nanoparticles made by the cluster gun. The zero field-cooled (ZFC) and field-cooled (FC) M(T) curves at different fields show that the blocking temperature is shifted to lower temperature when the applied magnetic field is increased. This behavior could be due to a decreased energy barrier at increased filed or to inter-particle dipole-dipole interactions. M vs H/T data above the blocking temperature show that the latter might be responsible for this behavior. The dynamics of the FC magnetization were also studied. The M(T) curves on FC samples obtained with the magnetic field on and off at different temperatures, show that the sample remembered its thermal history and demonstrated a memory effect at temperatures lower than the blocking temperature. However, this memory effects were not observed in the ZFC samples. The magnetic relaxation with a change at low temperature also shows a memory effect at temperature below the blocking temperature. The M(T) curves at different fields and memory effects indicate that the dynamics of nanoparticles are due to the distribution of particle sizes and inter-particle interactions. Work Supported by NSF GRANT # DMR-0302544.

Liu, Peng; Bonder, Michael; Hadjipanayis, George

2008-03-01

300

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

301

Impurity modes in Frenkel exciton systems with dipolar interactions and cubic symmetry  

NASA Astrophysics Data System (ADS)

We introduce a continuum model for impurity modes of Frenkel excitons in fully occupied face-centered and body-centered cubic lattices with dipole-dipole interactions and parallel moments. In the absence of impurities, the model reproduces the small-k behavior found in numerical calculations of dipolar lattice sums. The exciton densities of states near the upper and lower band edges are calculated and compared with the corresponding results for a random array of dipoles. The Green function obtained with the continuum model, together with a spherical approximation to the Brillouin zone, is used to determine the conditions for the formation of a localized exciton mode associated with a shift in the transition energy of a single chromophore. The dependence of the local mode energy on the magnitude of the shift is ascertained. The formation of impurity bands at high concentrations of perturbed sites is investigated using the coherent potential approximation. The contribution of the impurity bands to the optical absorption is calculated in the coherent potential approximation. The locations of the optical absorption peaks of the dipolar system are shown to depend on the direction of propagation of the light relative to the dipolar axis, a property that is maintained in the presence of short-range interactions.

Avgin, I.; Huber, D. L.

2013-04-01

302

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

303

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

304

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

305

Modeling Intermolecular Interactions in Nanotubes, Fullerenes and Graphite using a New Long-Range Potential  

NASA Technical Reports Server (NTRS)

The cohesive energy and compressibility of strands of a single-wall nanotube rope has been computed using a new long-range potential energy function derived from accurate ab initio quantum chemistry calculations of the benzene dimer and calibrated for energetic and mechanical properties of graphite (at pressures up to 12 GPa). We also use this potential to calculate a variety of properties of carbon nanotubes (both single- and multi-wall) and fullerenes. Extensive comparisons are made with previously published potentials.

Jaffe, Richard; Halicioglu, Timur; Han, Jie; Yang, Liu; Huo, Winifred (Technical Monitor)

1998-01-01

306

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

307

Intermolecular interactions and water structure in a condensed phase B-DNA crystal  

Microsoft Academic Search

By controlled dehydration, the unit cells of dodecamer DNA-drug crystals have been shrunk from 68 000 (normal state) to 60 000 (partially dehydrated intermediate state) to 51 000 Å3 (fully dehydrated state), beyond which no further solvent loss occurs. The total solvent content in the normal crystals is ~40% by volume, reducing to ~20% in the fully dehy- drated phase.

George R. Clark; Christopher J. Squire; L. J. Baker; Roger F. Martin; Jonathan White

2000-01-01

308

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

309

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

2014-10-21

310

Gels from a semifluorinated n-alkane in fluorinated solvents as a probe for intermolecular interactions  

Microsoft Academic Search

Diblock semifluorinated n-alkanes can form aggregates and gels in fluorinated solvents. We have investigated the thermal behavior of binary mixtures comprising F(CF2)8(CH2)16H and fluorinated solvents. The solvents were perfluorohexane, perfluoroheptane, perfluorooctane, perfluorooctyl bromide, perfluorodecalin, and perfluorotributylamine. The phase diagrams were used to calculate the activity coefficients of the two components and the main excess thermodynamic functions. The solubility and self-assembly

Lorenzo Tattini; Pierandrea Lo Nostro; Luca Scalise; Barry W. Ninham; Piero Baglioni

2009-01-01

311

Role of intermolecular interactions in fabricating hardened electro-optic materials  

Microsoft Academic Search

Until recently, the product of chromophore dipole moment, (mu) , and molecular first hyperpolarizability, (beta) , divided by chromophore molecular weight was considered to be an appropriate chromophore figure of merit. Substantial progress has been made designing and synthesizing chromophores characterized by large (mu) (beta) values. If such high (mu) (beta) chromophores could be translated to hardened acentric polymer lattices

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

1997-01-01

312

HIGH SENSITIVITY FOURIER TRANSFORM NMR. INTERMOLECULAR INTERACTIONS BETWEEN ENVIRONMENTAL TOXIC SUBSTANCES AND BIOLOGICAL MACROMOLECULES  

EPA Science Inventory

This project explored the feasibility of developing new techniques for evaluation of the effects of environmental toxic materials on complex biopolymer systems using high sensitivity Fourier transform nuclear magnetic resonance (nmr) spectroscopy. Commercial instrumentation avail...

313

Intermolecular repulsion through interfacial attraction: toward engineering of polymorphs.  

PubMed

Understanding the formation of crystalline polymorphs is of importance for various applications of materials science. Polymorphism of Schiff base derivatives has recently attracted considerable attention because of its influence on photochromic and thermochromic properties of their 3D crystals. The present investigation extends the study of Schiff base polymorphism to the molecular level by using a combination of scanning tunneling microscopy at the liquid/solid interface and molecular modeling. It is demonstrated that polymorphism of 4-(dodecyloxy)-N-(4-dodecylphenyl)-2-hydroxybenzaldimine (PHB), a Schiff base substituted by alkyl side chains, can occur in 2D crystals when PHB is adsorbed on a surface that is able to exchange charge with the molecule. In particular, on Au(111), PHB molecules self-organize not only into a columnar packing but also in dimer structures. Theoretical and experimental results demonstrate that the dimer-based structure observed on Au(111) originates from molecule/surface interactions, which in turn modify molecule/molecule interactions. The results highlight that the Au(111) substrate is far from being a passive part of the self-assembled system and plays a crucial role in the morphology of 2D polymorphs. PMID:19827775

Kudernac, Tibor; Sändig, Nadja; Fernández Landaluce, Tatiana; van Wees, Bart J; Rudolf, Petra; Katsonis, Nathalie; Zerbetto, Francesco; Feringa, Ben L

2009-11-01

314

Quantitative Relation between Intermolecular and Intramolecular Binding of Pro-Rich Peptides to SH3 Domains  

E-print Network

Quantitative Relation between Intermolecular and Intramolecular Binding of Pro-Rich Peptides to SH3 linkers: 1), intramolecular binding of proline-rich peptides (PRPs) to SH3 domains for kinase regulation; 2), intramolecular binding of PRP for increasing the folding stability of SH3 domains; and 3

Weston, Ken

315

A novel intermolecular synthesis of ?-lactones via visible-light photoredox catalysis.  

PubMed

Direct ?-lactone formation via visible-light photoredox catalysis has been achieved efficiently including hydroxylalkylation of aromatic alkenes and transesterification. The present photocatalytic protocol has good regioselectivity and substrate compatibility, affording a novel way to intermolecular ?-lactone synthesis by the reaction of styrenes with ?-bromo esters in the absence of any external oxidants. PMID:24215594

Wei, Xiao-Jing; Yang, Deng-Tao; Wang, Lin; Song, Tao; Wu, Li-Zhu; Liu, Qiang

2013-12-01

316

Stress acidulated amphoteric molecules and mechanochromism via reversible intermolecular proton transfer.  

PubMed

Stress has been proved to acidulate amphoteric molecules and promote an intermolecular proton transfer, which results in a significant absorption and emission change. The stress acidulated amphoteric molecules open a new avenue for developing mechanochromic materials and anticipate many broad applications such as stress/pressure sensors and rewritable media. PMID:23712461

Wang, Yi; Li, Minjie; Zhang, Yumo; Yang, Jin; Zhu, Shaoyin; Sheng, Lan; Wang, Xudong; Yang, Bing; Zhang, Sean Xiao-An

2013-07-28

317

Energetics of Homogeneous Intermolecular Vinyl and Allyl Carbon-Hydrogen Bond Activation by the  

E-print Network

Energetics of Homogeneous Intermolecular Vinyl and Allyl Carbon-Hydrogen Bond Activation by the 16 to devel- oping homogeneous transition-metal catalysts that ac- tivate and functionalize C-H bonds to the development of a viable homogeneous catalyst is a thorough understanding of the origin of the selectivities

Jones, William D.

318

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

NASA Astrophysics Data System (ADS)

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; Wu, Ten-Ming

2013-11-01

319

One pot and selective intermolecular aryl- and heteroaryl-trifluoromethylation of alkenes by photoredox catalysis.  

PubMed

We report herein the first photoredox-catalyzed intermolecular aryl- and heteroaryltrifluoromethylation of alkenes. Under the optimized conditions using Umemoto's reagent as a CF3 source, a wide range of styrenes can be readily difunctionalized, affording the corresponding trifluoromethylated adducts in up to 99% yield. PMID:25285576

Carboni, Aude; Dagousset, Guillaume; Magnier, Emmanuel; Masson, Géraldine

2014-10-21

320

Intermolecular Potentials, Internal Motions, and Spectra of van der Waals and Hydrogen-Bonded Complexes  

E-print Network

directly and sensitively on the potential that holds such a complex together. As the intermolecular forces 4131 6.1.1. Atom-Linear Molecule Dimers 4131 6.1.2. Ar-Benzene 4132 6.1.3. Trimers and Larger Clusters

321

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

322

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

323

Intermolecular bonding and vibrations of phenol?H2O (D2O)  

NASA Astrophysics Data System (ADS)

Extensive ab initio calculations of the phenol?H2O complex were performed at the Hartree-Fock level, using the 6-31G(d,p) and 6-311++G(d,p) basis sets. Fully energy-minimized geometries were obtained for (a) the equilibrium structure, which has a translinear H bond and the H2O plane orthogonal to the phenol plane, similar to (H2O)2; (b) the lowest-energy transition state structure, which is nonplanar (C1 symmetry) and has the H2O moiety rotated by ±90°. The calculated MP2/6-311G++(d,p) binding energy including basis set superposition error corrections is 6.08 kcal/mol; the barrier for internal rotation around the H bond is only 0.4 kcal/mol. Intra- and intermolecular harmonic vibrational frequencies were calculated for a number of different isotopomers of phenol?H2O. Anharmonic intermolecular vibrational frequencies were computed for several intermolecular vibrations; anharmonic corrections are very large for the ?2 intermolecular wag. Furthermore, the H2O torsion ? around the H-bond axis, and the ?2 mode are strongly anharmonically coupled, and a two-dimensional ?/?2 potential energy surface was explored. The role of tunneling splitting due to the torsional mode is discussed and tunnel splittings are estimated for the calculated range of barriers. The theoretical studies were complemented by a detailed spectroscopic study of h-phenol?H2O and d-phenol?D2O employing two-color resonance-two-photon ionization and dispersed fluorescence emission techniques, which extends earlier spectroscopic studies of this system. The ?1 and ?2 wags of both isotopomers in the S0 and S1 electronic states are newly assigned, as well as several other weaker transitions. Tunneling splittings due to the torsional mode may be important in the S0 state in conjunction with the excitation of the intermolecular ? and ?2 modes.

Schütz, Martin; Bürgi, Thomas; Leutwyler, Samuel; Fischer, Thomas

1993-03-01

324

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

325

Detection and characterization of individual intermolecular bonds using optical tweezers.  

PubMed Central

The development of scanning probe techniques has made it possible to examine protein-protein interactions at the level of individual molecular pairs. A calibrated optical tweezers, along with immunoglobulin G (IgG)-coated polystyrene microspheres, has been used to detect individual surface-linked Staphylococcus protein A (SpA) molecules and to characterize the strength of the noncovalent IgG-SpA bond. Microspheres containing, on average, less than one IgG per contact area were held in the optical trap while an SpA-coated substrate was scanned beneath them at a distance of approximately 50 nm. This geometry allows the trapped bead to make contact with the surface, from bond formation to rupture, and results in an enhancement of the force applied to a bond due to leverage supplied by the bead itself. Experiments yielded median single-bond rupture forces from 25 to 44 pN for IgG from four mammalian species, in general agreement with predictions based on free energies of association obtained from solution equilibrium constants. PMID:11371470

Stout, A L

2001-01-01

326

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

327

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

NASA Astrophysics Data System (ADS)

In this, the third part of our series on the dielectric spectrum symmetrical broadening of water, we consider the nucleotide aqueous solutions. Where in Parts I [E. Levy et al., J. Chem. Phys. 136, 114502 (2012), 10.1063/1.3687914] and II [E. Levy et al., J. Chem. Phys. 136, 114503 (2012), 10.1063/1.3691183], the dipole-dipole or ion-dipole interaction had a dominant feature, now the interplay between these two types of dipole-matrix interactions will be considered. We present the results of high frequency dielectric measurements of different concentrations of adenosine monophosphate/adenosine-5'-triphosphate aqueous solutions. We observed the Cole-Cole broadening of the main relaxation peak of the solvent in the solutions. Moreover, depending on the nucleotide concentration, we observed both types of dipole-matrix interaction. The 3D trajectory approach (described in detail in Part I) is applied in order to highlight the differences between the two types of interaction.

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

2012-11-01

328

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

E-print Network

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. Commonly this interaction is obtained by standard quantum mechanical perturbation theory to second order. However, the latter is restricted to electrostatic interactions between charges and 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 the statistical mechanical method the equivalence of the Casimir-Polder and van der Waals interactions to leading order for short separations where retardation effects can be neglected. Physically this is well known, but in our opinion the mathematics of this transition process is not so obvious. The evaluations needed mean a transform of the statistical mechanical free energy expression to a form that can be identified with second order perturbation theory. In recent works [H{\\o}ye 2010] the Casimir-Polder or Casimir energy has been added as a correction to calculations of systems like the electron clouds of molecules. The equivalence to van der Waals interactions to leading order indicates that the added Casimir energy will improve the accuracy of calculated molecular energies. We here also give numerical estimates of this energy including analysis and estimates for the uniform electron gas.

Johan S. Høye

2011-01-07

329

Intermolecular transmission of superoxide dismutase 1 misfolding in living cells  

PubMed Central

Human wild-type superoxide dismutase-1 (wtSOD1) is known to coaggregate with mutant SOD1 in familial amyotrophic lateral sclerosis (FALS), in double transgenic models of FALS, and in cell culture systems, but the structural determinants of this process are unclear. Here we molecularly dissect the effects of intracellular and cell-free obligately misfolded SOD1 mutant proteins on natively structured wild-type SOD1. Expression of the enzymatically inactive, natural familial ALS SOD1 mutations G127X and G85R in human mesenchymal and neural cell lines induces misfolding of wild-type natively structured SOD1, as indicated by: acquisition of immunoreactivity with SOD1 misfolding-specific monoclonal antibodies; markedly enhanced protease sensitivity suggestive of structural loosening; and nonnative disulfide-linked oligomer and multimer formation. Expression of G127X and G85R in mouse cell lines did not induce misfolding of murine wtSOD1, and a species restriction element for human wtSOD1 conversion was mapped to a region of sequence divergence in loop II and ?-strand 3 of the SOD1 ?-barrel (residues 24–36), then further refined surprisingly to a single tryptophan residue at codon 32 (W32) in human SOD1. Time course experiments enabled by W32 restriction revealed that G127X and misfolded wtSOD1 can induce misfolding of cell-endogenous wtSOD1. Finally, aggregated recombinant G127X is capable of inducing misfolding and protease sensitivity of recombinant human wtSOD1 in a cell-free system containing reducing and chelating agents; cell-free wtSOD1 conversion was also restricted by W32. These observations demonstrate that misfolded SOD1 can induce misfolding of natively structured wtSOD1 in a physiological intracellular milieu, consistent with a direct protein–protein interaction. PMID:21930926

Grad, Leslie I.; Guest, Will C.; Yanai, Anat; Pokrishevsky, Edward; O'Neill, Megan A.; Gibbs, Ebrima; Semenchenko, Valentyna; Yousefi, Masoud; Wishart, David S.; Plotkin, Steven S.; Cashman, Neil R.

2011-01-01

330

Long-Range Energy Transfer in the Case of Inhomogeneous Spatial Distributions and Indirect Donor-Donor Interaction  

NASA Astrophysics Data System (ADS)

On the basis of Förster kinetics concerning long-range energy transfer caused by dipole-dipole interaction the t-deactivation-law has been derived under the assumption of a homogeneous spatial acceptor distribution (at the end of the forties). Recently, in particular ultra-short time fluorescence and absorption measurements have shown that on the one hand this law holds in a wide range of physical conditions, but that under other circumstances the experimental results strongly deviate from the t-law. In the present paper it is shown that a unified treatment of inhomogeneous distributions and indirect donor-donor interaction via the acceptors can qualitatively, and in certain cases also quantitatively, remove the discrepancies mentioned. The analysis yields new parameters of dynamical processes.Translated AbstractEnergietransport über längere Entfernungen bei inhomogenen räumlichen Verteilungen und indirekter Donor-DonorwechselwirkungUnter der Annahme homogener, räumlicher Akzeptorverteilung wurde in den vierziger Jahren das t-Deaktivierungsgesetz auf der Basis einer Förster-Kinetik für langreichweitigen Energietransport durch Dipol-Dipolwechselwirkung abgeleitet. Besonders Kurzzeitfluoreszenz- und Absorptionsmessungen haben in letzter Zeit gezeigt, daß einerseits dieses Gesetz für eine große Zahl physikalischer Bedingungen gilt, unter besonderen Umständen die experimentellen Ergebnisse jedoch stark vom t-Gesetz abweichen. In der vorliegenden Arbeit wird gezeigt, daß eine einheitliche Behandlung inhomogener Verteilungen und indirekter Donor-Donorwechselwirkungen über die Akzeptoren qualitativ und in bestimmten Fällen auch quantitativ die erwähnten Unterschiede beseitigen kann. Die Analyse gibt neue Parameter des dynamischen Prozesses.

Schubert, Max

331

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

NASA Astrophysics Data System (ADS)

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.

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

2014-09-01

332

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

333

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

334

Intermolecular vibrations of different isotopologs of the water dimer: Experiments and density functional theory calculations  

NASA Astrophysics Data System (ADS)

Far infrared spectra of seven different isotopologs of the water dimer have been measured in neon matrices at 2.8 K. The experiments are interpreted with the aid of density functional theory calculations, in particular the calculated harmonic isotopic shifts were utilized. All six intermolecular vibrational modes of the water dimer and the fully deuterated water dimer are assigned based the isotopic shifts induced. 31 of a total of 42 intermolecular fundamental modes of the seven different H, D, and 18O containing water dimers have been experimentally observed and assigned accordingly. The overall agreement between the calculations and the experiments of all isotopologs results in a complete and consistent description of these modes.

Ceponkus, J.; Uvdal, P.; Nelander, B.

2008-11-01

335

Laser initiation thresholds of a 'green' aluminum\\/molybdenum-trioxide metastable intermolecular composite and other pyrotechnics  

Microsoft Academic Search

Metastable intermolecular composites (MIC) consisting of nanometer-scale aluminum and molybdenum trioxide have been proposed as fast initiators. A compound of this class of material was evaluated as a potential environmentally friendly replacement pyrotechnic material for lead styphnate for use in the primer of the M230 medium-caliber automatic cannon. In addition to removing the lead hazard, laser ignition would also reduce

Stephen L. Howard; Jeffrey B. Morris; Richard A. Beyer; Scott J. Hamlin; James Martin; Gregory C. Burke; Thomas Doris

2005-01-01

336

An intermolecular C-H functionalization method for the synthesis of 3-hydroxy-2-oxindoles.  

PubMed

An intermolecular C-H functionalization method is developed for the synthesis of 3-hydroxy-2-oxindoles. Rh(iii)-catalyzed N-nitroso-directed C-H addition to ethyl 2-oxoacetate allows subsequent denitrosation-triggered cyclization construction of 3-hydroxy-2-oxindoles. The method features a broad substrate scope and its synthetic utility is demonstrated on the synthesis of target compounds bearing functional groups (hydroxyl, bromo) amenable to further elaboration. PMID:25247749

Chen, Jinsen; Song, Chao; Chen, Pei; Zhu, Jin

2014-10-01

337

Estimate of the intermolecular polarization contribution to the static dielectric constant of water  

Microsoft Academic Search

In this paper, molecular-structure data derived from recent quantum-chemical studies are used in conjunction with the Mandel-Mazur theory of the static dielectric constant to estimate the importance of intermolecular polarization contributions to the static dielectric constant of water. A scalar expression for the static dielectric constant is identified and then investigated via a multibody decomposition in which the effects of

James W. Kress; John J. Kozak

1976-01-01

338

Cascade Intramolecular N-Arylation/Intermolecular Carboamination Reactions for the Construction of Tricyclic Heterocycles  

PubMed Central

A new method for the stereoselective synthesis of tetrahydropyrroloindoles and hexahydropyrroloquinolines of general structure 8 is described. These products are formed through cascade Pd-catalyzed coupling reactions between aryl chlorides and unsaturated amine substrates 5. A single catalyst effects an intramolecular N-arylation reaction followed by an intermolecular alkene carboamination reaction to generate two rings, three bonds, and one stereocenter with good chemoselectivity, diastereoselectivity, and chemical yield. PMID:21604733

Lemen, Georgia S.; Wolfe, John P.

2011-01-01

339

A computational analysis of ordering in 2O.4 based on quantum mechanics and intermolecular forces  

Microsoft Academic Search

A computational analysis of ordering in p-ethoxybenzylidene-p-n-butylaniline (2O.4) has been carried out based on quantum mechanics and intermolecular forces. The evaluation of atomic charges\\u000a and dipole moments at each atomic center has been carried out using the CNDO\\/2 method. The configuration energy has been computed\\u000a using the modified Rayleigh-Schrdinger perturbation method at an interval of 1 in translation and 10

D. P. Ojha

2006-01-01

340

Regioselective base-free intermolecular aminohydroxylations of hindered and functionalized alkenes.  

PubMed

Regioselective base-free intermolecular aminohydroxylations of functionalized trisubstituted and 1,1-disubstituted alkenes employing benzoyloxycarbamate 3a and catalytic OsO(4) are described. In all cases, the more substituted alcohol isomer is favored. Sluggish reactions could be promoted by gentle heating, the use of amine ligands, or increased catalyst loadings. A competitive rearrangement was observed with a secondary allylic alcohol substrate. The adducts serve as useful precursors to dehydroamino acids. PMID:22188212

Ma, Zhiwei; Naylor, Bradley C; Loertscher, Brad M; Hafen, Danny D; Li, Jasmine M; Castle, Steven L

2012-01-20

341

Direct observation of the intermolecular triplet-triplet energy transfer from UV-A absorber 4- tert -butyl-4?-methoxydibenzoylmethane to UV-B absorber octyl methoxycinnamate  

NASA Astrophysics Data System (ADS)

Triplet energy transfer (TET) is an important photostabilization process for organic UV absorbers, such as 4- tert-butyl-4'-methoxydibenzoylmethane (BM-DBM) and octyl methoxycinnamate (OMC). To characterize interactions between UV absorbers as TET the interactions between BM-DBM and OMC have been studied through measurements of EPR and time-resolved phosphorescence spectra. The EPR Bmin signals and the phosphorescence of OMC were observed through the selective excitation of BM-DBM at 365 nm in EtOH at 77 K. These results indicate that the intermolecular TET occurs from BM-DBM to OMC. This is the first report of the experimental evidence of the TET between the organic UV absorbers.

Kikuchi, Azusa; Yagi, Mikio

2011-09-01

342

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

343

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

344

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

345

Numerical modeling and interpretation of dipole-dipole resistivity and IP profiles Cove Fort-Sulphurdale KGRA, Utah  

Microsoft Academic Search

The Cove Fort-Sulphurdale Known Geothermal Resource Area (KGRA) is located near the junction of the Pavant Range and the Tushar Mountains in south-central Utah. The area has been the site of an intensive geothermal exploration effort since 1975. The electrical resistivity data obtained by Union Oil Company and a subsequent survey conducted for the Earth Science Laboratory and a detailed

1979-01-01

346

2442 IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION, VOL. 60, NO. 5, MAY 2012 Polarization Estimation With a Dipole-Dipole  

E-print Network

reveal attributes intrinsic to the emitter or the reflector, e.g., a star's photosphere asymmetry due to "limb polarization" [33]. Commonly used for polariza- tion-estimation are electrically short dipoles

Wong, Kainam Thomas

347

Intermolecular hydrogen bonded and self-assembled ?-pleated sheet structures of ?-sulfidocarbonyls  

NASA Astrophysics Data System (ADS)

The three crystal structures of ?-sulfidocarbonyls 1, 2 and 3 synthesized from the reaction of acryl amide with cystiene, 1,2-dithiol and 1,3-dithiols, respectively, in water catalyzed by borax, have been determined at 273 K. The characteristic features of the structures are self-assembly through intermolecular hydrogen bonding leading to infinite chains of molecules in one direction, in addition to the stacking of layers of such molecular chains in the perpendicular direction ultimately giving rise to ?-pleated sheets of 3D molecular network involving N-H⋯O, C-H⋯O and C-H⋯S bonding in the crystal lattice.

Hussain, Sahid; Das, Gopal; Chaudhuri, Mihir K.

2007-06-01

348

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

349

A general approach to mechanism in multiproduct reactions: product-specific intermolecular kinetic isotope effects.  

PubMed

Here we report a general method for the measurement of (13)C kinetic isotope effects at natural abundance for reactions that yield two or more products concurrently. We use, as an example, a recently reported Co-catalyzed reaction between cyclopentene and 1-phenyl-1-propyne. High-precision intermolecular (13)C isotope effects are reported for both the formal [2+2] cycloaddition (major) and Alder-ene (minor) reaction products. Mechanistic possibilities that are in accord with observed isotope effect measurements are discussed. PMID:24721128

Xiang, Shuhuai; Meyer, Matthew P

2014-04-23

350

Quantum interference and local field effects in a medium of V-type three-level atoms  

Microsoft Academic Search

We study the intrinsic optical bistability displayed by a small sample of $V$-type three-level atoms induced by the near dipole-dipole interaction. The use of the coherent state properties in the limit of the generalized second-order Born approximation for BBGKY-hierarchy of equations for the reduced density operators allows one to derive the operator describing the near dipole-dipole interaction (local field correction)

M. G. Gladush; A. A. Panteleev; Vl. K. Roerich

2004-01-01

351

Non-linear QCD dynamics in two-photon interactions at high energies  

SciTech Connect

Assuming that the dipole - dipole cross section can be related with the dipole - proton cross section, we calculate the total {gamma}{gamma}, {gamma}*{gamma}* cross-sections and the real photon structure function F{sup {gamma}}{sub 2}(x,Q{sup 2}) using the recent solution of the BK equation with running coupling constant.

Carvalho, F. [Depto de Ciencias Exatas e da Terra, Universidade Federal de Sao Paulo Rua Arthur Riedel 275, Jd. Eldorado, Cep 09972-270, Diadema, SP (Brazil); Navarra, F. S.; Cazaroto, E. [Instituto de Fisica, Universidade de Sao Paulo, Rua do Matao, Travessa R, 187, 05508-090 Sao Paulo, SP (Brazil); Goncalves, V. P. [Instituto de Fisica e Matematica, Universidade Federal de Pelotas Caixa Postal 354, 96010-900, Pelotas, RS (Brazil)

2013-03-25

352

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

353

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil.  

PubMed

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH?O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented. PMID:24632154

Ç?rak, Ça?r?; Sert, Yusuf; Ucun, Fatih

2014-06-01

354

Foot-and-mouth disease virus leader proteinase: Structural insights into the mechanism of intermolecular cleavage  

PubMed Central

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 Lpro (Labpro and Lbpro). These forms free themselves from the viral polyprotein by intra- and intermolecular self-processing and subsequently cleave the cellular eukaryotic initiation factor (eIF) 4G. During infection, Lbpro removes six residues from its own C-terminus, generating sLbpro. We present the structure of sLbpro bound to the inhibitor E64-R-P-NH2, illustrating how sLbpro can cleave between Lys/Gly and Gly/Arg pairs. In intermolecular cleavage on polyprotein substrates, Lbpro was unaffected by P1 or P1? substitutions and processed a substrate containing nine eIF4GI cleavage site residues whereas sLbpro failed to cleave the eIF4GI containing substrate and cleaved appreciably more slowly on mutated substrates. Introduction of 70 eIF4GI residues bearing the Lbpro binding site restored cleavage. These data imply that Lbpro and sLbpro may have different functions in infected cells. PMID:25240326

Steinberger, Jutta; Grishkovskaya, Irina; Cencic, Regina; Juliano, Luiz; Juliano, Maria A.; Skern, Tim

2014-01-01

355

Intermolecular Forces as a Key to Understanding the Environmental Fate of Organic Xenobiotics  

NASA Astrophysics Data System (ADS)

Environmental education for undergraduate nonscience majors and high school students is key in fostering an increased understanding of environmental issues among the general public. We have developed an environmental chemistry module that can be used in high schools or undergraduate nonscience courses to relate chemical structures and properties to the macroscopic behavior of environmentally relevant organic chemicals like pesticides, PCBs, and solvents. The module introduces the concepts of intermolecular forces, polarity, and partitioning to explain complex phenomena such as environmental transport and biomagnification of xenobiotics (human-made chemicals). The level 1 version 2.11 model, developed by Trent University, is used in a laboratory segment that allows students to explore the relationship between chemical properties and environmental distribution. The initial material on polarity and intermolecular forces can lead to additional applications, including: bioaccumulation and biomagnification of organic chemicals; toxicology or pharmacology (ability of molecules to cross membranes); and groundwater contamination. This module can enhance chemistry courses by presenting detailed applications and allowing students to make powerful, verifiable predictions. See Featured Molecules .

Casey, Ryan E.; Pittman, Faith A.

2005-02-01

356

Hydration and distance dependence of intermolecular shearing between collagen molecules in a model microfibril.  

PubMed

In vertebrates, collagen tissues are the main component responsible for force transmission. In spite of the physiological importance of these phenomena, force transmission mechanisms are still not fully understood, especially at smaller scales, including in particular collagen molecules and fibrils. Here we investigate the mechanism of molecular sliding between collagen molecules within a fibril, by shearing a central molecule in a hexagonally packed bundle mimicking the collagen microfibril environment, using varied lateral distance between the molecules in both dry and solvated conditions. In vacuum, the central molecule slides under a stick-slip mechanism that is due to the characteristic surface profile of collagen molecules, enhanced by the breaking and reformation of H-bonds between neighboring collagen molecules. This mechanism is consistently observed for varied lateral separations between molecules. The high shearing force (>7 nN) found for the experimentally observed intermolecular distance (?1.1 nm) suggests that in dry samples the fibril elongation mechanism relies almost exclusively on molecular stretching, which may explain the higher stiffnesses found in dry fibrils. When hydrated, the slip-stick behavior is observed only below 1.3 nm of lateral distance, whereas above 1.3 nm the molecule shears smoothly, showing that the water layer has a strong lubricating effect. Moreover, the average force required to shear is approximately the same in solvated as in dry conditions (?2.5 nN), which suggests that the role of water at the intermolecular level includes the transfer of load between molecules. PMID:22762892

Gautieri, Alfonso; Pate, Monica I; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J

2012-08-01

357

?-? Interactions and magnetic properties in a series of hybrid inorganic-organic crystals  

NASA Astrophysics Data System (ADS)

The series of hybrid inorganic-organic solids T(Im)2[Ni(CN)4] with T=Fe, Co, Ni and Im=imidazole were prepared by soft chemical routes from aqueous solutions of the involved building units: imidazole, T2+ metal and the [Ni(CN)4]2- anionic block. The obtained samples were characterized from infrared and UV-vis spectroscopies, and thermogravimetric, X-ray diffraction and magnetic measurements. Anhydrous solids which crystallize with a monoclinic unit cell, in the I2/a space group with four formula units per cell (Z=4) were obtained. Their crystal structure was solved ab initio from the recorded X-ray powder patterns and then refined by the Rietveld method. The metal T is found with octahedral coordination to four N ends of CN groups and two imidazole molecules while the inner Ni atom preserves its planar coordination. The system of layers remains stacked in an ordered 3D structure through dipole-dipole and ?-? interactions between imidazole rings from neighboring layers. In this way, a pillared structure is achieved without requiring the coordination of both nitrogen atoms from imidazole ring. The recorded magnetic data indicate the occurrence of a predominant ferromagnetic interaction at low temperature for Co and Ni but not for Fe. Such magnetic ordering is more favorable for Ni with transition temperature of 14.67 K, which was ascribed to the relatively high polarizing power for this metal. Within the considered T metals, to nickel the highest electron-withdrawing ability corresponds and this leads to an increase for the metal-ligand electron clouds overlapping and to a stronger ?-? attractive interaction, two factors that result into a higher magnetic ordering temperature.

González, M.; Lemus-Santana, A. A.; Rodríguez-Hernández, J.; Knobel, M.; Reguera, E.

2013-01-01

358

Density functional theory calculations on dipeptide gallic acid interaction  

NASA Astrophysics Data System (ADS)

In the present investigation, an attempt has been made to study the interaction of dipeptides with gallic acid, using Becke3 parameter Lee Yang Parr (B3LYP) method employing 3-21G*, 6-31G* and 6-31+G* basis sets. The interaction energies of the dipeptide-gallic acid complexes are in the range of -5 to -18 kcal/mol depending on the mode of intermolecular complexation. Calculated molecular electrostatic potential (MESP) for the various intermolecular complexes revealed the electrostatic nature of the interaction. Qualitative estimations based on chemical hardness and chemical potential demonstrated fractional electron transfer from dipeptide to gallic acid.

Madhan, B.; Parthasarathi, R.; Subramanian, V.; Raghava Rao, J.; Nair, Balachandran Unni; Ramasami, T.

2003-02-01

359

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

360

Reciprocity theory of gas surface interactions  

Microsoft Academic Search

Since the Direct Simulation Monte Carlo (DSMC) method has established itself as a standard technique for numerically computing rarefied gas flows, it follows that to develop the theory of rarefied gas dynamics a framework for its fundamental microscopic processes needs to be formulated, i.e., intermolecular collisions and gas surface interactions, which lead to rigorous statistical models that can be utilized

Adolf A. Agbormbai

1989-01-01

361

Thrombin receptor activation. Confirmation of the intramolecular tethered liganding hypothesis and discovery of an alternative intermolecular liganding mode.  

PubMed

Cleavage of the thrombin receptor's amino-terminal exodomain at the Arg41/Ser42 peptide bond within the sequence ... LDPR41/S42FLLRN ... is necessary and sufficient for receptor activation by proteases. The synthetic peptide SFLLRN activates the receptor independent of proteolysis. We proposed that the SFLLRN sequence is a tethered peptide ligand; receptor cleavage unmasks this agonist which then binds intramolecularly to effect receptor activation. The alternative hypothesis that receptor cleavage or exogenous SFLLRN effect receptor activation by disrupting tonic inhibitory interactions exerted by the receptor's amino-terminal exodomain has not been excluded. We report that delta AMINO, a mutant thrombin receptor lacking the amino-terminal exodomain, was not constitutively active and responded to SFLLRN but not thrombin when expressed in Xenopus oocytes or mammalian cells. Thrombin signaling was restored when delta AMINO was co-expressed with ATE-CD8 which encoded the receptor's amino-terminal exodomain fused to the transmembrane domain of CD8. Co-expression of a thrombin receptor lacking a functional tethered ligand domain ("F43A") with a non-signaling receptor mutant bearing an intact tethered ligand domain ("YYY") also reconstituted thrombin signaling. However, the EC50 for thrombin activation of cells co-expressing F43A and YYY was > 1000-fold that for cells expressing comparable levels of wild type receptor, while EC50s for activation by SFLLRN were similar. These and other data refute the release from inhibition hypothesis and suggest that while intermolecular liganding between two thrombin receptor molecules can occur, the intramolecular tethered liganding mechanism is the predominant mode of thrombin receptor activation. PMID:8206902

Chen, J; Ishii, M; Wang, L; Ishii, K; Coughlin, S R

1994-06-10

362

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

363

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

364

Raman Q-branch line shapes as a test of the H2-Ar intermolecular potential  

NASA Technical Reports Server (NTRS)

The line-shape cross sections of vibrational Raman Q-branch spectra are determined theoretically for D2 and H2 in Ar. The calculations are based on accurate close-coupling matrices and the intermolecular potential obtained by Le Roy and Hutson (1987) from spectra of van der Waals complexes. The calculation techniques applied are explained, and the results are presented in tables and graphs and discussed in detail with reference to published experimental data. Agreement to within about 25 percent is obtained for the line widths, but the line shifts are found to be a factor of two smaller than the measured values, and a temperature dependence of line-width cross sections is predicted which is not observed experimentally.

Green, Sheldon

1990-01-01

365

Identification of cyanogen bromide peptides involved in intermolecular cross-linking of bovine type III collagen.  

PubMed Central

Cyanogn bromide peptides derived from bovine type III collagen and containing reducible cross-links were isolated and identified. Two peptides, alpha 1 (III)CB7 and alpha 1 (III)CB9B, from within the helical portion of the molecule were shown to contain the 'amino donor' residues cross-linked to non-helical 'aldehyde donor' residues in the formation of cross-links. This information, in conjunction with previously published data for the order of the cyanogen bromide peptides [Fietzek, Allman, Rauterberg & Wachter (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 84-86], suggests that in type III collagen intermolecular cross-links are located in the end-overlap regions, so as to stabilize a quarter-stagger arrangement of molecules within the fibre in a similar manner to that proposed for type I and type II collagens. PMID:6769428

Nicholls, A C; Bailey, A J

1980-01-01

366

Sequence-specific electron injection into DNA from an intermolecular electron donor.  

PubMed

Electron transfer in DNA has been intensively studied to elucidate its biological roles and for applications in bottom-up DNA nanotechnology. Recently, mechanisms of electron transfer to DNA have been investigated; however, most of the systems designed are intramolecular. Here, we synthesized pyrene-conjugated pyrrole-imidazole polyamides (PPIs) to achieve sequence-specific electron injection into DNA in an intermolecular fashion. Electron injection from PPIs into DNA was detected using 5-bromouracil as an electron acceptor. Twelve different 5-bromouracil-containing oligomers were synthesized to examine the electron-injection ability of PPI. Product analysis demonstrated that the electron transfer from PPIs was localized in a range of 8 bp from the binding site of the PPIs. These results demonstrate that PPIs can be a useful tool for sequence-specific electron injection. PMID:23439569

Morinaga, Hironobu; Takenaka, Tomohiro; Hashiya, Fumitaka; Kizaki, Seiichiro; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

2013-04-01

367

Azide-water intermolecular coupling measured by 2-color 2D IR spectroscopy  

NASA Astrophysics Data System (ADS)

We present 2-color two-dimensional infrared spectroscopy of intermolecular coupling between azide ions and their solvation shell water molecules. The cross-peak between azide asymmetric stretch vibration and the OD-stretch vibration is a result of low- probability uphill population transfer. Narrow bleach/excited state absorption peak shows selectivity to solvation shell water molecules only and the characteristics of the cross-peak suggest that the solvation shell hydrogen bond potential has similar anharmonic properties as the hydrogen bond in ice Ih. Population and depopulation of the excited state of the OD-stretch vibration happen on 150 fs and 1.7 ps timescales, respectively, with early manifesting heating effects that limit the selectivity to population times up to 1 ps.

Borek, J. A.; Perakis, F.; Hamm, P.

2013-03-01

368

Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths  

NASA Astrophysics Data System (ADS)

Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

Gu, Quanli; Trindle, Carl; Knee, J. L.

2012-09-01

369

The intermolecular structure of phosphoric acid-N,N-dimethylformamide mixtures as studied by computer simulation  

NASA Astrophysics Data System (ADS)

The computer simulation of H3PO4-N,N-dimethylformamide (DMF) mixtures over the whole concentration range using molecular dynamic (MD) methods has been carried out. The preferential orientations of the nearest neighbors of H3PO4 and DMF molecules were obtained using the ranked radial distribution functions technique. On the basis of MD results, the parameters of hydrogen bonds between molecules in mixture were calculated. The changes of the intermolecular structure of mixture as a function of acid composition over the whole concentration range were analyzed and reported. Analysis of O...H distance distributions and angles between O-H (H3PO4) and C=O (DMF) or P=O (H3PO4) vector distributions showed that O(DMF) and O(H3PO4) may each have two hydrogen bonds.

Fedorova, Irina V.; Kiselev, Michael G.; Safonova, Lyubov P.

2011-05-01

370

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

371

Competing intramolecular NH⋯OC hydrogen bonds and extended intermolecular network in 1-(4-chlorobenzoyl)-3-(2-methyl-4-oxopentan-2-yl) thiourea analyzed by experimental and theoretical methods  

NASA Astrophysics Data System (ADS)

The synthesis of a novel 1-acyl-thiourea species (C14H17N2O2SCl), has been tailored in such a way that two distinct NH⋯OC intramolecular competing hydrogen bonds are feasible. The X-ray structure analysis as well as the vibrational (FT-IR and FT-Raman) data reveal that the S conformation is preferred, with the CO and CS bonds of the acyl-thiourea group pointing in opposite directions. The preference for the intramolecular NH⋯OC hydrogen bond within the C(O)NHC(S)NH core is confirmed. The Natural Bond Orbital and the Atom in Molecule approaches demonstrate that a strong hyperconjugative lpO ? ??(NH) remote interaction between the acyl and the thioamide NH groups is responsible for the stabilization of the S conformation. Intermolecular interactions have been characterized in the periodic system electron density and the topological analysis reveals the presence of an extended intermolecular network in the crystal, including a Cl⋯N interaction playing a relevant role in crystal packing.

Saeed, Aamer; Khurshid, Asma; Jasinski, Jerry P.; Pozzi, C. Gustavo; Fantoni, Adolfo C.; Erben, Mauricio F.

2014-03-01

372

A convergent intermolecular Diels-Alder approach to the spirocycles found in the marine neurotoxic agents, the gymnodimines  

E-print Network

of the spirocyclic core structure of the gymnodimines was achieved in 7 linear steps and 16.4% overall yield from diethyl malonate. The key step in the synthesis was a Lewis-acid promoted intermolecular Dials-Alder reaction of an N-tosyl ?-methylene []-lactam and a...

Cohn, Stephen Todd

2012-06-07

373

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

374

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

E-print Network

envisioned that hydroamination of unactivated olefins might be catalyzed by gold complexes, as well. WeGold(I)-Catalyzed Intra- and Intermolecular Hydroamination of Unactivated Olefins Junliang Zhang report here the gold(I)- mediated hydroamination of inert olefins to afford acyclic or cyclic nitrogen

He, Chuan

375

The human immunodeficiency virus type 1 envelope glycoprotein precursor acquires aberrant intermolecular disulfide bonds that may prevent normal proteolytic processing.  

PubMed

The envelope glycoprotein of human immunodeficiency virus consists of two subunits, designated gp120 and gp41, derived from the cleavage of a precursor polypeptide gp160. When expressed from a recombinant vaccinia virus and analyzed by velocity gradient sedimentation and polyacrylamide gel electrophoresis, a significant proportion of gp160 molecules formed oligomers that were stabilized by intermolecular disulfide bonds. Oligomeric forms of both gp120 and gp41 were also observed, but these oligomers were noncovalently associated. Both the intermolecularly linked oligomers of gp160 and the unlinked oligomeric envelope protein subunits were found to accumulate with time. These results indicate that there are two populations of gp160 precursors, one that is folded and processed correctly into gp120 and gp41 and another that is intermolecularly disulfide bonded and remains uncleaved. We propose that the formation of intermolecular disulfide bonds is not an intermediate step in the maturation of the envelope glycoprotein, but rather a result of misfolding of the gp160 precursor which prevents it from being properly processed. PMID:2238472

Owens, R J; Compans, R W

1990-12-01

376

EDTA-Derivatized Deoxythymidine as a Tool for Rapid Determination of Protein Binding Polarity to DNA by Intermolecular Paramagnetic Relaxation  

E-print Network

Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland overlap in the sugar region of the DNA 1H NMR spectrum, a low density of protons on the DNA, lack manner, the polarity of protein binding could be determined by observing intermolecular PRE effects

Clore, G. Marius

377

PHYSICAL REVIEW B 83, 245307 (2011) Optical evidence for intermolecular coupling in mixed films of pentacene and perfluoropentacene  

E-print Network

-acceptor interface in solar cells. In such systems the effects of intermolecular coupling on the optical, electronic mixing ratios of PFP:PEN (1:4, 1:2, 1:1, 2:1, and 4:1) were chosen. Before film growth the temperatures serves as a p-n junction. Those effects can be efficiently studied in systems that exhibit intermixing

Schreiber, Frank

378

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

379

Engineered two-dimensional Ising interactions in a trapped-ion quantum simulator with hundreds of spins.  

PubMed

The presence of long-range quantum spin correlations underlies a variety of physical phenomena in condensed-matter systems, potentially including high-temperature superconductivity. However, many properties of exotic, strongly correlated spin systems, such as spin liquids, have proved difficult to study, in part because calculations involving N-body entanglement become intractable for as few as N???30 particles. Feynman predicted that a quantum simulator--a special-purpose 'analogue' processor built using quantum bits (qubits)--would be inherently suited to solving such problems. In the context of quantum magnetism, a number of experiments have demonstrated the feasibility of this approach, but simulations allowing controlled, tunable interactions between spins localized on two- or three-dimensional lattices of more than a few tens of qubits have yet to be demonstrated, in part because of the technical challenge of realizing large-scale qubit arrays. Here we demonstrate a variable-range Ising-type spin-spin interaction, J(i,j), on a naturally occurring, two-dimensional triangular crystal lattice of hundreds of spin-half particles (beryllium ions stored in a Penning trap). This is a computationally relevant scale more than an order of magnitude larger than previous experiments. We show that a spin-dependent optical dipole force can produce an antiferromagnetic interaction J(i,j) proportional variant d(-a)(i,j), where 0???a???3 and d(i,j) is the distance between spin pairs. These power laws correspond physically to infinite-range (a = 0), Coulomb-like (a = 1), monopole-dipole (a = 2) and dipole-dipole (a = 3) couplings. Experimentally, we demonstrate excellent agreement with a theory for 0.05???a???1.4. This demonstration, coupled with the high spin count, excellent quantum control and low technical complexity of the Penning trap, brings within reach the simulation of otherwise computationally intractable problems in quantum magnetism. PMID:22538611

Britton, Joseph W; Sawyer, Brian C; Keith, Adam C; Wang, C-C Joseph; Freericks, James K; Uys, Hermann; Biercuk, Michael J; Bollinger, John J

2012-04-26

380

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile.  

PubMed

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. PMID:24287056

Agarwal, Parag; Bee, Saba; Gupta, Archana; Tandon, Poonam; Rastogi, V K; Mishra, Soni; Rawat, Poonam

2014-01-01

381

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

382

Laser initiation thresholds of a 'green' aluminum/molybdenum-trioxide metastable intermolecular composite and other pyrotechnics  

NASA Astrophysics Data System (ADS)

Metastable intermolecular composites (MIC) consisting of nanometer-scale aluminum and molybdenum trioxide have been proposed as fast initiators. A compound of this class of material was evaluated as a potential environmentally friendly replacement pyrotechnic material for lead styphnate for use in the primer of the M230 medium-caliber automatic cannon. In addition to removing the lead hazard, laser ignition would also reduce or remove certain hazards due to electrostatic or radio frequency radiation. This study was conducted with both a flashlamp-pumped Nd+3:YAG laser and a fiber-coupled diode laser. The measured threshold ignition energies of the MIC and two other inorganic pyrotechnic compounds are presented. The low ignition threshold, advances in diode laser technology, and compact size of the diode laser indicated that laser diode technology could be an ideal candidate ignition source for the M230 cannon. The candidate pyrotechnic compounds were also evaluated for suitability in laser initiation via measurement of time-to-first-light. This metric provided a measurement of the potential for achievement of the necessary action time required for proper cannon operation.

Howard, Stephen L.; Morris, Jeffrey B.; Beyer, Richard A.; Hamlin, Scott J.; Martin, James; Burke, Gregory C.; Doris, Thomas

2005-09-01

383

Rates of intra- and intermolecular electron transfers in hydrogenase deduced from steady-state activity measurements.  

PubMed

Electrons are transferred over long distances along chains of FeS clusters in hydrogenases, mitochondrial complexes, and many other respiratory enzymes. It is usually presumed that electron transfer is fast in these systems, despite the fact that there has been no direct measurement of rates of FeS-to-FeS electron transfer in any respiratory enzyme. In this context, we propose and apply to NiFe hydrogenase an original strategy that consists of quantitatively interpreting the variations of steady-state activity that result from changing the nature of the FeS clusters which connect the active site to the redox partner, and/or the nature of the redox partner. Rates of intra- and intermolecular electron transfer are deduced from such large data sets. The mutation-induced variations of electron transfer rates cannot be explained by changes in intercenter distances and reduction potentials. This establishes that FeS-to-FeS rate constants are extremely sensitive to the nature and coordination of the centers. PMID:21615141

Dementin, Sébastien; Burlat, Bénédicte; Fourmond, Vincent; Leroux, Fanny; Liebgott, Pierre-Pol; Abou Hamdan, Abbas; Léger, Christophe; Rousset, Marc; Guigliarelli, Bruno; Bertrand, Patrick

2011-07-01

384

Intermolecular proton shuttling in excited state proton transfer reactions: insights from theory.  

PubMed

The mechanism of base to base intermolecular proton shuttling occurring in the excited state proton transfer reaction between 7-hydroxy-4-(trifluoromethyl)coumarin (CouOH) and concentrated 1-methylimidazole base (1-MeId) in toluene solution is disclosed here by means of a computational approach based on Density Functional Theory (DFT) and Time Dependent DFT (TD-DFT). These methods allow us to characterize both the ground and excited state potential energy surfaces along the proton shuttling coordinate, and to assess the nature of the emitting species in the presence of an excess of 1-MeId. As a result, the tautomerism of CouOH is found to be photo-activated and, from a mechanistic point of view, the calculations clearly show that the overall driving force of the entire shuttling is the coumarin photoacidity, which is responsible for both the first proton transfer event and the strengthening of the following chain mechanism of base to base proton hopping. PMID:24676232

Savarese, Marika; Netti, Paolo A; Rega, Nadia; Adamo, Carlo; Ciofini, Ilaria

2014-05-14

385

Site- and energy-selective slow-electron production through intermolecular Coulombic decay  

NASA Astrophysics Data System (ADS)

Irradiation of matter with light tends to electronically excite atoms and molecules, with subsequent relaxation processes determining where the photon energy is ultimately deposited and electrons and ions produced. In weakly bound systems, intermolecular Coulombic decay (ICD) enables very efficient relaxation of electronic excitation through transfer of the excess energy to neighbouring atoms or molecules that then lose an electron and become ionized. Here we propose that the emission site and energy of the electrons released during this process can be controlled by coupling the ICD to a resonant core excitation. We illustrate this concept with ab initio many-body calculations on the argon-krypton model system, where resonant photoabsorption produces an initial or `parent' excitation of the argon atom, which then triggers a resonant-Auger-ICD cascade that ends with the emission of a slow electron from the krypton atom. Our calculations show that the energy of the emitted electrons depends sensitively on the initial excited state of the argon atom. The incident energy can thus be adjusted both to produce the initial excitation in a chosen atom and to realize an excitation that will result in the emission of ICD electrons with desired energies. These properties of the decay cascade might have consequences for fundamental and applied radiation biology and could be of interest in the development of new spectroscopic techniques.

Gokhberg, Kirill; Koloren?, P?emysl; Kuleff, Alexander I.; Cederbaum, Lorenz S.

2014-01-01

386

Site- and energy-selective slow-electron production through intermolecular Coulombic decay.  

PubMed

Irradiation of matter with light tends to electronically excite atoms and molecules, with subsequent relaxation processes determining where the photon energy is ultimately deposited and electrons and ions produced. In weakly bound systems, intermolecular Coulombic decay (ICD) enables very efficient relaxation of electronic excitation through transfer of the excess energy to neighbouring atoms or molecules that then lose an electron and become ionized. Here we propose that the emission site and energy of the electrons released during this process can be controlled by coupling the ICD to a resonant core excitation. We illustrate this concept with ab initio many-body calculations on the argon-krypton model system, where resonant photoabsorption produces an initial or 'parent' excitation of the argon atom, which then triggers a resonant-Auger-ICD cascade that ends with the emission of a slow electron from the krypton atom. Our calculations show that the energy of the emitted electrons depends sensitively on the initial excited state of the argon atom. The incident energy can thus be adjusted both to produce the initial excitation in a chosen atom and to realize an excitation that will result in the emission of ICD electrons with desired energies. These properties of the decay cascade might have consequences for fundamental and applied radiation biology and could be of interest in the development of new spectroscopic techniques. PMID:24362566

Gokhberg, Kirill; Koloren?, P?emysl; Kuleff, Alexander I; Cederbaum, Lorenz S

2014-01-30

387

Pressure waves generated by metastable intermolecular composites in an aqueous environment  

NASA Astrophysics Data System (ADS)

In the present study, pressure waves generated by a metastable intermolecular composite (MIC) have been measured experimentally in an aqueous environment and correlated with flame speed measurements. Underwater experiments were performed in a 1.0 L high-pressure chamber mounted with high-resolution pressure transducers and designed with optical access. Samples consisting of a stoichiometric mixture of aluminium and copper(II)-oxide particles were evaluated. Two types of samples were synthesized; a mixture of micron-sized raw powders, and ball-milled powders with a fine-scale nano-structure. A planetary mill was used to refine reactant powders from micron- to nano-scale dimensions. The dynamics of the pressure wave and high-pressure gas bubble were monitored via pressure histories and high-speed Schlieren visualization. The effect of reactant particle size has been evaluated quantitatively. The dynamics of the pressure wave were correlated with the rate of expansion of the high-pressure gas bubble.

Maines, G.; Radulescu, M.; Bacciochini, A.; Jodoin, B.; Lee, J. J.

2014-05-01

388

Intermolecular potentials and the accurate prediction of the thermodynamic properties of water  

SciTech Connect

The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au [Centre for Molecular Simulation, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122 (Australia)

2013-11-21

389

Intermolecular potentials and the accurate prediction of the thermodynamic properties of water  

NASA Astrophysics Data System (ADS)

The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm3 for a wide range of temperatures (298-650 K) and pressures (0.1-700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

Shvab, I.; Sadus, Richard J.

2013-11-01

390

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

PubMed

A new formulation of the second-order exchange-induction energy of symmetry-adapted perturbation theory is presented. In the proposed formalism the exchange-induction energy is expressed through one- and two-particle reduced density matrices of monomers, which are of zeroth and first order with respect to the effective electrostatic potential of another monomer. The resulting expression is further modified by using the partition of two-particle density matrices into the antisymmetrized product of one-particle density matrices and the remaining cumulant part. The proposed formalism has been applied to the case of closed-shell monomers and for density matrices obtained from the expectation-value expression with coupled cluster singles and doubles wave functions. The performance of the new approach has been demonstrated on several benchmark van der Waals systems, including dimers of argon, water, and ethyne. PMID:18979036

Korona, Tatiana

2008-11-21

391

Hole - Nuclear Spin Interaction in Semiconductor Quantum Dots  

NASA Astrophysics Data System (ADS)

Spins of localized electrons in semiconductor quantum dots (QDs) are attractive for future spintronic and quantum information devices since they are not subject to the classical spin relaxation mechanisms known for free carriers [1]. It is now well established that the main spin dephasing mechanism in QDs is due to the coupling of conduction electron spin with the randomly fluctuating nuclear spins (Fermi contact term) [2-5]. For a valence electron (or hole), this coupling is expected to be much weaker because of the p-symmetry of the valence band states and no experimental evidence of such a hole-nuclear spin interaction has been reported so far [6]. We have measured the carrier spin dynamics in p-doped InAs/GaAs quantum dots by pump probe and time-resolved photoluminescence experiments. We demonstrate that the hole spin dynamics in these QDs is governed by the interaction with randomly fluctuating nuclear spins [7]. Our calculations based on dipole-dipole coupling between the hole and the quantum dot nuclei lead to a hole spin dephasing time for an ensemble of dots of 15 ns in close agreement with experiments.[4pt] In collaboration with B. Eble, C. Testelin, F. Bernardot, and M. Chamarro, Institut des Nanosciences de Paris, Universit'e P. et M. Curie, CNRS, Paris, F-75015 France; A. Balocchi, T. Amand, and B. Urbaszek, Universit'e de Toulouse ; LPCNO, INSA-CNRS-UPS, 135 av. de Rangueil, 31077 Toulouse Cedex 4, France; and A. Lemaître, Laboratoire de Photonique et de Nanostructures, CNRS, Route de Nozay, F-91460, Marcoussis, France. [4pt] [1] Spin Physics in Semiconductors, edited by M. D'Yakonov (Springer, Berlin, 2008) [0pt] [2] I. Merkulov et al, Phys. Rev. B 65, 205309 (2002) [0pt] [3] P.-F. Braun, X. Marie et al, PRL 94, 116601 (2005) [0pt] [4] A. C. Johnson et al , Nature 435, 925 (2005) [0pt] [5] A. Greilich et al, Science 313, 341(2006) [0pt] [6] S. Laurent et al, Phys. Rev. Lett. 94, 147401 (2005) [0pt] [7] B. Eble et al, Phys. Rev. Lett. 102, 146601 (2009)

Marie, Xavier

2010-03-01

392

Detecting intermolecular NOEs by means of a novel DPFGSE pulse sequence. Application to the solvation of carbohydrates in binary mixtures  

NASA Astrophysics Data System (ADS)

We present a pulse sequence based on solute-to-solvent NOE enhancement and aimed at the detection of intermolecular NOE's. Thus, a W3 pulse cluster is used to selectively filter the solvent signals in a DPFGSE sequence. The sequence has been tested on a sample of glucose dissolved in two binary aqueous mixtures (water-acetonitrile and water-DMSO). We show how the resulting enhancements may derive from intermolecular cross-relaxation or, in the water-DMSO sample, also from chemical exchange. In each case, a quantitative interpretation of the data is also supplied, both in terms of local enrichment in one specific solvent (preferential solvation), and by means of a kinetic model for a two-site chemical exchange.

Bagno, Alessandro; Rastrelli, Federico; Scorrano, Gianfranco

2004-03-01

393

Hydrogen bonding interactions of ?-phenylcinnamic acid isomers in the liquid phase studied by IR and NMR spectroscopies and computational methods  

Microsoft Academic Search

Intra- and intermolecular hydrogen bonding interactions of ?-phenylcinnamic acid isomers were studied in the solution phase by infrared (IR) and proton nuclear magnetic resonance (1H NMR) spectroscopies and the AM1 semi-empirical method. The solvents were CDCl3 or dimethyl sulfoxide (DMSO), the concentration of the acid isomers were varied. Spectroscopic measurements revealed that (i) intermolecular hydrogen bonds are typical for both

I. Pálinkó; B. Török; M. Rózsa-Tarjányi; J. T. Kiss; Gy. Tasi

1995-01-01

394

Time-Resolved and Micro-Scale Measurement of Thermal Property for Intermolecular Dynamics Using an Infrared Laser  

NASA Astrophysics Data System (ADS)

This paper describes a time-resolved measurement of thermal property in microscale during reaction processes of polymer by using an infrared (IR) laser. Polymer or gel-like material, so-called macromolecules, have diversity in its structure and intermolecular association, and recent development of measurement and control technique in micro- and nano- scale has opened up new possibilities for the property design of materials. The intermolecular dynamics of polymer can be reflected in time-resolved information of the thermal conductivity or thermal diffusivity. A measurement system of the thermal diffusivity in real-time and non-contact manner based on the forced Rayleigh scattering (FRS) method has been developed. This system can be applied for a changing process of a wide variety of polymer material because of employing a CO2 laser with the IR wavelength. Also, it is possible to measure the micro-scale property. By using the IR-FRS system, an investigation of the relationship between intermolecular dynamics of macromolecules and energy transfer can be conducted through the time-resolved data of the thermal diffusivity. As samples, crosslinking processes of a polysaccharide aqueous solution and an ultraviolet curable polymer were measured. In these processes, the samples change their microstructure by hydrogen and covalent bonding, respectively. Time evolution of the measured thermal property from the IR-FRS system clearly indicated the difference in bonding modes of macromolecules. According to the time-resolved measurement results, the validity of this technique for a versatile instrument of intermolecular dynamics of macromolecules is demonstrated.

Motosuke, Masahiro; Nagasaka, Yuji; Honami, Shinji

395

One-pot stereoselective synthesis of ?,?-differentiated diamino esters via the sequence of aminochlorination, aziridination and intermolecular SN2 reaction.  

PubMed

We report here an efficient one-pot method for the synthesis of ?,?-differentiated diamino esters directly from cinnamate esters using N,N-dichloro-p-toluenesulfonamide and benzylamine as nitrogen sources. The key transformations include a Cu-catalyzed aminohalogenation and aziridination, followed by an intermolecular SN2 nucleophilic ring opening by benzylamine. The reactions feature a wide scope of substrates and proceed with excellent stereo- and regioselectivity (anti:syn >99:1) . PMID:25161740

Xiong, Yiwen; Qian, Ping; Cao, Chenhui; Mei, Haibo; Han, Jianlin; Li, Guigen; Pan, Yi

2014-01-01

396

Diastereoselective intermolecular ene reactions: synthesis of 4,5,6,7-tetrahydro-1H-benzo[d]imidazoles.  

PubMed

The Diels-Alder cycloadducts of 4-vinylimidazoles and N-phenylmaleimide are shown to undergo facile intermolecular ene reactions. Overall the reaction of three simple molecules (a diene, a dienophile and an enophile) in a two-step process gives 4,5,6,7-tetrahydro-1H-benzo[d]imidazoles with high yields, high atom economy and diastereocontrol of up to 5 new stereocentres. PMID:22801593

Watson, Lynsey J; Harrington, Ross W; Clegg, William; Hall, Michael J

2012-09-01

397

LINGO, an efficient holographic text based method to calculate biophysical properties and intermolecular similarities.  

PubMed

SMILES strings are the most compact text based molecular representations. Implicitly they contain the information needed to compute all kinds of molecular structures and, thus, molecular properties derived from these structures. We show that this implicit information can be accessed directly at SMILES string level without the need to apply explicit time-consuming conversion of the SMILES strings into molecular graphs or 3D structures with subsequent 2D or 3D QSPR calculations. Our method is based on the fragmentation of SMILES strings into overlapping substrings of a defined size that we call LINGOs. The integral set of LINGOs derived from a given SMILES string, the LINGO profile, is a hologram of the SMILES representation of the molecule described. LINGO profiles provide input for QSPR models and the calculation of intermolecular similarities at very low computational cost. The octanol/water partition coefficient (LlogP) QSPR model achieved a correlation coefficient R2=0.93, a root-mean-square error RRMS=0.49 log units, a goodness of prediction correlation coefficient Q2=0.89 and a QRMS=0.61 log units. The intrinsic aqueous solubility (LlogS) QSPR model achieved correlation coefficient values of R2=0.91, Q2=0.82, and RRMS=0.60 and QRMS=0.89 log units. Integral Tanimoto coefficients computed from LINGO profiles provided sharp discrimination between random and bioisoster pairs extracted from Accelrys Bioster Database. Average similarities (LINGOsim) were 0.07 for the random pairs and 0.36 for the bioisosteric pairs. PMID:15807504

Vidal, David; Thormann, Michael; Pons, Miquel

2005-01-01

398

Investigation of the intermolecular recognition mechanism between the E3 ubiquitin ligase Keap1 and substrate based on multiple substrates analysis.  

PubMed

E3 ubiquitin ligases are attractive drug targets due to their specificity to the ubiquitin machinery. However, the development of E3 ligase inhibitors has proven challenging for the fact that they must disrupt protein-protein interactions (PPIs). The E3 ligase involved in interactome provide new hope for the discovery of the E3 ligase inhibitors. These currently known natural binding partners of the E3 ligase can benefit the discovery of other unknown substrates and also the E3 ligase inhibitors. Herein, we present a novel strategy that using multiple substrates to elucidate the molecular recognition mechanism of E3 ubiquitin ligase. Molecular dynamics simulation, molecular mechanics-generalized born surface area (MM-GBSA) binding energy calculation and energy decomposition scheme were incorporated to evaluate the quantitative contributions of sub-pocket and per-residue to binding. In this case, Kelch-like ECH-associated protein-1 (Keap1), a substrate adaptor component of the Cullin-RING ubiquitin ligases complex, is applied for the investigation of how it recognize its substrates, especially Nrf2, a master regulator of the antioxidant response. By analyzing multiple substrates binding determinants, we found that both the polar sub-pockets (P1 and P2) and the nonpolar sub-pockets (P4 and P5) of Keap1 can make remarkable contributions to intermolecular interactions. This finding stresses the requirement for substrates to interact with the polar and nonpolar sub-pockets simultaneously. The results discussed in this paper not only show the binding determinants of the Keap1 substrates but also provide valuable implications for both Keap1 substrate discovery and PPI inhibitor design. PMID:25301376

Jiang, Zheng-Yu; Xu, Li-Li; Lu, Meng-Chen; Pan, Yang; Huang, Hao-Ze; Zhang, Xiao-Jin; Sun, Hao-Peng; You, Qi-Dong

2014-12-01

399

Nickel-catalyzed intermolecular reductive couplings of alkynes and aldehydes ; Enantioselective synthesis of (-)-terpestacin and structural revision of siccanol using catalytic stereoselective fragment couplings and macrocyclizations  

E-print Network

I. Nickel-Catalyzed Intermolecular Reductive Coupling of Alkynes and Aldehydes. Alkynes and aldehydes were coupled reductively in a single catalytic reaction to yield di- and trisubstituted allylic alcohols with high ...

Chan, Johann, 1976-

2004-01-01

400

Structures of hydrazones, (E)-2-(1,3-benzothiazolyl)-NHsbnd Ndbnd CHsbnd Ar, [Ar = 4-(pyridin-2-yl)phenyl, pyrrol-2-yl, thien-2-yl and furan-2-yl]: Difference in conformations and intermolecular hydrogen bonding  

NASA Astrophysics Data System (ADS)

Structures of hydrazones, (E)-2-(1,3-benzothiazolyl)-NHsbnd Ndbnd CHsbnd Ar(Ar = pyridine-2-yl (1), pyrrol-2-yl (2), thien-2-yl (3) and furan-2-yl (4), prepared from 2-hydrazinyl-1,3-benzothiazole and ArCHO, followed by recrystallisation from alcohol solutions, are reported. No significant intramolecular hydrogen bonds are present in any of the four molecules. Different conformations were found between 2 and 3, on one hand and for 4, on the other. Thus for 4, the oxygen atom of the furanyl ring is on the same side of the molecule as is the sulfur atom of the benzothiazole unit, while in contrast, each of the heteroatoms of the thienyl and pyrrole rings lies on opposite sides to the benzothiazole sulphur atom. In addition to the conformational variations, differences are noted in the connections between molecules. Despite the presence in each case of N(hydrazono)sbnd H---N(benzothiazolo) intermolecular hydrogen bonds, molecules of 4 are linked into spiral chains, while molecules of 2 and 3 (and indeed all compounds having Ar = substituted phenyl) form symmetric dimers. Further intermolecular interactions, albeit weaker ones, are found in 2 [Csbnd H··N and Nsbnd H··?], 3 [Csbnd H··?] and 4 [?··?], while dimers of 1 remain essentially free. Calculations carried out using the DFT(B3LYP)/6-311++G(d,p) method indicated that the conformations determined by crystallography for 2-4 were the more stable.

Lindgren, Eric B.; Yoneda, Julliane D.; Leal, Katia Z.; Nogueira, Antônio F.; Vasconcelos, Thatyana R. A.; Wardell, James L.; Wardell, Solange M. S. V.

2013-03-01

401

Contrasting intermolecular and intramolecular exciplex formation of a 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad.  

PubMed

An intramolecular exciplex is formed upon excitation of the cyclohexane solution of the 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad, but little if any intramolecular CT complex exists in the ground state of this substance in solution. In contrast, in the crystalline state, the dyad forms an intermolecular mixed-stack CT complex in the ground state and an intermolecular exciplex when it is photoexcited. PMID:20353197

Imoto, Mitsutaka; Ikeda, Hiroshi; Fujii, Takayuki; Taniguchi, Hisaji; Tamaki, Akihiro; Takeda, Motonori; Mizuno, Kazuhiko

2010-05-01

402

Kinetic isotope effects in cytochrome p-450-catalyzed oxidation reactions. intermolecular and intramolecular deuterium isotope effects during the n-demethylation of n,n-dimethylphentermine  

Microsoft Academic Search

Two N,N-dimethylphentermine (N,N-dimethyl-2-amino-2-methyl-3-phenylpropane) substrates differing in deuterium substitution have been used to determine the intermolecular and intramolecular isotope effects associated with the cytochrome P-450-dependent N-demethylation of this substrate. No intermolecular isotope effect was observed in Vmax or Vmax\\/Km when the reaction rates for this substrate were compared to those for the substrate in which both N-methyl groups contained deuterium. In

G. T. Miwa; W. A. Garland; B. J. Hodshon; A. Y. Lu; D. B. Northrop

1980-01-01

403

Collective many-body van der Waals interactions in molecular systems  

E-print Network

proper- ties. Cases studied include the binding affinity of ellipticine, a DNA- intercalating anticancer agent, the relative energetics between the A- and B-conformations of DNA, and the thermodynamic for in molecular simulations. intermolecular interactions dispersion interactions force fields DNA stability

404

Mechanochemical mechanism for fast reaction of metastable intermolecular composites based on dispersion of liquid metal  

NASA Astrophysics Data System (ADS)

An unexpected mechanism for fast reaction of Al nanoparticles covered by a thin oxide shell during fast heating is proposed and justified theoretically and experimentally. For nanoparticles, the melting of Al occurs before the oxide fracture. The volume change due to melting induces pressures of 1-2 GPa and causes dynamic spallation of the shell. The unbalanced pressure between the Al core and the exposed surface creates an unloading wave with high tensile pressures resulting in dispersion of atomic scale liquid Al clusters. These clusters fly at high velocity and their reaction is not limited by diffusion (this is the opposite of traditional mechanisms for micron particles and for nanoparticles at slow heating). Physical parameters controlling the melt dispersion mechanism are found by our analysis. In addition to an explanation of the extremely short reaction time, the following correspondence between our theory and experiments are obtained: (a) For the particle radius below some critical value, the flame propagation rate and the ignition time delay are independent of the radius; (b) damage of the oxide shell suppresses the melt dispersion mechanism and promotes the traditional diffusive oxidation mechanism; (c) nanoflakes react more like micron size (rather than nanosize) spherical particles. The reasons why the melt dispersion mechanism cannot operate for the micron particles or slow heating of nanoparticles are determined. Methods to promote the melt dispersion mechanism, to expand it to micron particles, and to improve efficiency of energetic metastable intermolecular composites are formulated. In particular, the following could promote the melt dispersion mechanism in micron particles: (a) Increasing the temperature at which the initial oxide shell is formed; (b) creating initial porosity in the Al; (c) mixing of the Al with a material with a low (even negative) thermal expansion coefficient or with a phase transformation accompanied by a volume reduction; (d) alloying the Al to decrease the cavitation pressure; (e) mixing nano- and micron particles; and (f) introducing gasifying or explosive inclusions in any fuel and oxidizer. A similar mechanism is expected for nitridation and fluorination of Al and may also be tailored for Ti and Mg fuel.

Levitas, Valery I.; Asay, Blaine W.; Son, Steven F.; Pantoya, Michelle

2007-04-01

405

Intramolecular and lateral intermolecular hole transfer at the sensitized TiO2 interface.  

PubMed

Characterization of the redox properties of TiO2 interfaces sensitized to visible light by a series of cyclometalated ruthenium polypyridyl compounds containing both a terpyridyl ligand with three carboxylic acid/carboxylate or methyl ester groups for surface binding and a tridentate cyclometalated ligand with a conjugated triarylamine (NAr3) donor group is described. Spectroelectrochemical studies revealed non-Nernstian behavior with nonideality factors of 1.37 ± 0.08 for the Ru(III/II) couple and 1.15 ± 0.09 for the NAr3(•+/0) couple. Pulsed light excitation of the sensitized thin films resulted in rapid excited-state injection (k(inj) > 10(8) s(-1)) and in some cases hole transfer to NAr3 [TiO2(e(-))/Ru(III)-NAr3 ? TiO2(e(-))/Ru(II)-NAr3(•+)]. The rate constants for charge recombination [TiO2(e(-))/Ru(III)-NAr3 ? TiO2/Ru(II)-NAr3 or TiO2(e(-))/Ru(II)-NAr3(•+) ? TiO2/Ru(II)-NAr3] were insensitive to the identity of the cyclometalated compound, while the open-circuit photovoltage was significantly larger for the compound with the highest quantum yield for hole transfer, behavior attributed to a larger dipole moment change (?? = 7.7 D). Visible-light excitation under conditions where the Ru(III) centers were oxidized resulted in injection into TiO2 [TiO2/Ru(III)-NAr3 + h? ? TiO2(e(-))/Ru(III)-NAr3(•+)] followed by rapid back interfacial electron transfer to another oxidized compound that had not undergone excited-state injection [TiO2(e(-))/Ru(III)-NAr3 ? TiO2/Ru(II)-NAr3]. The net effect was the photogeneration of equal numbers of fully reduced and fully oxidized compounds. Lateral intermolecular hole hopping (TiO2/Ru(II)-NAr3 + TiO2/Ru(III)-NAr3(•+) ? 2TiO2/Ru(III)-NAr3) was observed spectroscopically and was modeled by Monte Carlo simulations that revealed an effective hole hopping rate of (130 ns)(-1). PMID:24367914

Hu, Ke; Robson, Kiyoshi C D; Beauvilliers, Evan E; Schott, Eduardo; Zarate, Ximena; Arratia-Perez, Ramiro; Berlinguette, Curtis P; Meyer, Gerald J

2014-01-22

406

Solute-solvent intermolecular vibronic coupling as manifested by the molecular near-field effect in resonance hyper-Raman scattering  

NASA Astrophysics Data System (ADS)

Vibronic coupling within the excited electronic manifold of the solute all-trans-?-carotene through the vibrational motions of the solvent cyclohexane is shown to manifest as the ``molecular near-field effect,'' in which the solvent hyper-Raman bands are subject to marked intensity enhancements under the presence of all-trans-?-carotene. The resonance hyper-Raman excitation profiles of the enhanced solvent bands exhibit similar peaks to those of the solute bands in the wavenumber region of 21 700-25 000 cm-1 (10 850-12 500 cm-1 in the hyper-Raman exciting wavenumber), where the solute all-trans-?-carotene shows a strong absorption assigned to the 1Ag --> 1Bu transition. This fact indicates that the solvent hyper-Raman bands gain their intensities through resonances with the electronic states of the solute. The observed excitation profiles are quantitatively analyzed and are successfully accounted for by an extended vibronic theory of resonance hyper-Raman scattering that incorporates the vibronic coupling within the excited electronic manifold of all-trans-?-carotene through the vibrational motions of cyclohexane. It is shown that the major resonance arises from the B-term (vibronic) coupling between the first excited vibrational level (v = 1) of the 1Bu state and the ground vibrational level (v = 0) of a nearby Ag state through ungerade vibrational modes of both the solute and the solvent molecules. The inversion symmetry of the solute all-trans-?-carotene is preserved, suggesting the weak perturbative nature of the solute-solvent interaction in the molecular near-field effect. The present study introduces a new concept, ``intermolecular vibronic coupling,'' which may provide an experimentally accessible/theoretically tractable model for understanding weak solute-solvent interactions in liquid.

Shimada, Rintaro; Hamaguchi, Hiro-O.

2011-01-01

407

Palladium-Catalyzed Intermolecular Oxyvinylcyclization of Alkenes with Alkynes: An Approach to 3-Methylene ?-Lactones and Tetrahydrofurans.  

PubMed

A novel chloropalladation-initiated intermolecular oxyvinylcyclization of alkenes with alkynoic acids or alkynols is developed. This protocol provides a series of 3-methylene ?-lactone and tetrahydrofuran derivatives in moderate to excellent yields with high stereoselectivities in the presence of PdCl2 and CuCl2 or CuCl2·2H2O. Besides a broad substrate scope, this method has the advantages of mild reaction conditions and easily accessible starting materials. Furthermore, the construction of C-Cl, C(sp(2))-C(sp(3)), and C-O bonds in one step was also achieved in this transformation. PMID:25215554

Zhang, Zhenming; Ouyang, Lu; Wu, Wanqing; Li, Jianxiao; Zhang, Zhicai; Jiang, Huanfeng

2014-11-21

408

Binding of G-Quadruplex-interactive Agents to Distinct G-Quadruplexes Induces Different Biological Effects in MiaPaCa Cells  

Microsoft Academic Search

Our previous studies have demonstrated the preference of telomestatin for intramolecular, rather than the intermolecular, G-quadruplex structures, while TMPyP4 has selectivity for intermolecular over intramolecular G-quadruplex structures. However, it was not clear whether the difference in the selectivity between two different G-quadruplex-interactive agents could determine the corresponding biological effects in cultured human tumor cells. Here we evaluated the biological effects

Weijun Liu; Daekyu Sun; Laurence H. Hurley

2005-01-01

409

Predictive models for estimating the vapor pressure of poly- and perfluorinated compounds at different temperatures  

NASA Astrophysics Data System (ADS)

Poly- and perfluorinated compounds (PFCs) are a class of global environmental pollutants that are of concern regarding their environmental fate and adverse effects. However, data on the basic physicochemical property of PFCs are still limited. To fill part of the data gaps, temperature-dependent predictive models for vapor pressure of PFCs were developed based on previously reported experimental data. The applicability domain of the models was analyzed using the Williams plot and the influential points and the response outliers were identified. The statistical performance of the models was significantly improved by removing these influential points and response outliers. This procedure confirmed the importance of properly defining the applicability domain of the predictive models. It is shown that the main factors governing the vapor pressure of PFCs, are intermolecular dispersive interactions, hydrogen bonding, temperature, intermolecular dipole-induced dipole interactions and dipole-dipole interactions. Although the model obtained could be used to reliably predict the vapor pressures of certain PFCs at different temperatures, it is essential that the prediction must fall within the applicability domain of the model and the temperature range for reliable predictions.

Ding, Guanghui; Shao, Mihua; Zhang, Jing; Tang, Junyi; Peijnenburg, Willie J. G. M.

2013-08-01

410