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Sample records for intermolecular dynamics studied

  1. Intermolecular dynamics studied by paramagnetic tagging

    Xu Xingfu; Keizers, Peter H. J. [Leiden University, Institute of Chemistry (Netherlands); Reinle, Wolfgang; Hannemann, Frank; Bernhardt, Rita [Universitaet des Saarlandes, Naturwissenschaftlich-Technische Fakultaet III, Institut fuer Biochemie (Germany); Ubbink, Marcellus [Leiden University, Institute of Chemistry (Netherlands)], E-mail: m.ubbink@chem.leidenuniv.nl

    2009-04-15

    Yeast cytochrome c and bovine adrenodoxin form a dynamic electron transfer complex, which is a pure encounter complex. It is demonstrated that the dynamic nature of the interaction can readily be probed by using a rigid lanthanide tag attached to cytochrome c. The tag, Caged Lanthanide NMR Probe 5, induces pseudocontact shifts and residual dipolar couplings and does not perturb the binding interface. Due to the dynamics in the complex, residual dipolar couplings in adrenodoxin are very small. Simulation shows that cytochrome c needs to sample a large part of the surface of adrenodoxin to explain the small degree of alignment observed for adrenodoxin. The applied method provides a simple and straightforward way to observe dynamics in protein complexes or domain-domain mobility without the need for external alignment media.

  2. Intermolecular dynamics studied by paramagnetic tagging

    Xu Xingfu; Keizers, Peter H. J.; Reinle, Wolfgang; Hannemann, Frank; Bernhardt, Rita; Ubbink, Marcellus

    2009-01-01

    Yeast cytochrome c and bovine adrenodoxin form a dynamic electron transfer complex, which is a pure encounter complex. It is demonstrated that the dynamic nature of the interaction can readily be probed by using a rigid lanthanide tag attached to cytochrome c. The tag, Caged Lanthanide NMR Probe 5, induces pseudocontact shifts and residual dipolar couplings and does not perturb the binding interface. Due to the dynamics in the complex, residual dipolar couplings in adrenodoxin are very small. Simulation shows that cytochrome c needs to sample a large part of the surface of adrenodoxin to explain the small degree of alignment observed for adrenodoxin. The applied method provides a simple and straightforward way to observe dynamics in protein complexes or domain-domain mobility without the need for external alignment media

  3. Intra- und intermolecular hydrogen bonds. Spectroscopic, quantum chemical and molecular dynamics studies

    Simperler, A.

    1999-03-01

    Intra- and intermolecular H-bonds have been investigated with spectroscopic, quantum chemical, and molecular dynamics methods. The work is divided into the following three parts: 1. Intramolecular interactions in ortho-substituted phenols. Theoretical and experimental data that characterizes the intramolecular hydrogen bonds in 48 different o-substituted phenols are discussed. The study covers various kinds of O-H ... Y -type interactions (Y= N, O, S, F, Cl, Br, I, C=C, C=-C, and C-=N). The bond strength sequences for several series of systematically related compounds as obtained from IR spectroscopy data (i.e., v(OH) stretching frequencies) are discussed and reproduced with several theoretical methods (B3LYP/6-31G(d,p), B3LYP/6-311G(d,p), B3LYP/6-31++G(d,p), B3LYP/DZVP, MP2/6-31G(d,p), and MP2/6-31++G(d,p) levels of theory). The experimentally determined sequences are interpreted in terms of the intrinsic properties of the molecules: hydrogen bond distances, Mulliken partial charges, van der Waals radii, and electron densities of the Y-proton acceptors. 2. Competitive hydrogen bonds and conformational equilibria in 2,6-disubstituted phenols containing two different carbonyl substituents. The rotational isomers of ten unsymmetrical 2,6-disubstituted phenols as obtained by combinations of five different carbonyl substituents (COOH, COOCH 3 , CHO, COCH 3 , and CONH 2 ) have been theoretically investigated at the B3LYP/6-31G(d,p) level of theory. The relative stability of four to five conformers of each compound were determined by full geometry optimization for free molecules as well as for molecules in reaction fields with dielectric constants up to ε=37.5. A comparison with IR spectroscopic data of available compounds revealed excellent agreement with the theoretically predicted stability sequences and conformational equilibria. The stability of a conformer could be interpreted to be governed by the following two contributions: (i) an attractive hydrogen bond

  4. Intermolecular interaction studies of glyphosate with water

    Manon, Priti; Juglan, K. C.; Kaur, Kirandeep; Sethi, Nidhi; Kaur, J. P.

    2017-07-01

    The density (ρ), viscosity (η) and ultrasonic velocity (U) of glyphosate with water have been measured on different ultrasonic frequency ranges from 1MHz, 2MHz, 3MHz & 5MHz by varying concentrations (0.05%, 0.10%, 0.15%, 0.20%, 0.25%, 0.30%, 0.35%, & 0.40%) at 30°C. The specific gravity bottle, Ostwald's viscometer and quartz crystal interferometer were used to determine density (ρ), viscosity (η) and ultrasonic velocity (U). These three factors contribute in evaluating the other parameters as acoustic impedance (Z), adiabatic compressibility (β), relaxation time (τ), intermolecular free length (Lf), free volume (Vf), ultrasonic attenuation (α/f2), Rao's constant (R), Wada's constant (W) and relative strength (R). Solute-solvent interaction is confirmed by ultrasonic velocity and viscosity values, which increases with increase in concentration indicates stronger association between solute and solvent molecules. With rise in ultrasonic frequency the interaction between the solute and solvent particles decreases. The linear variations in Rao's constant and Wada's constant suggest the absence of complex formation.

  5. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

    Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

    2014-12-11

    The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

  6. Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.

    Yagasaki, Takuma; Saito, Shinji

    2009-09-15

    Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is

  7. Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials.

    Kreck, Cara A; Mancera, Ricardo L

    2014-02-20

    Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials.

  8. Polyelectrolyte brushes in mixed ionic medium studied via intermolecular forces

    Farina, Robert; Laugel, Nicolas; Pincus, Philip; Tirrell, Matthew

    2011-03-01

    The vast uses and applications of polyelectrolyte brushes make them an attractive field of research especially with the growing interest in responsive materials. Polymers which respond via changes in temperature, pH, and ionic strength are increasingly being used for applications in drug delivery, chemical gating, etc. When polyelectrolyte brushes are found in either nature (e.g., surfaces of cartilage and mammalian lung interiors) or commercially (e.g., skin care products, shampoo, and surfaces of medical devices) they are always surrounded by mixed ionic medium. This makes the study of these brushes in varying ionic environments extremely relevant for both current and future potential applications. The polyelectrolyte brushes in this work are diblock co-polymers of poly-styrene sulfonate (N=420) and poly-t-butyl styrene (N=20) which tethers to a hydrophobic surface allowing for a purely thermodynamic study of the polyelectrolyte chains. Intermolecular forces between two brushes are measured using the SFA. As multi-valent concentrations are increased, the brushes collapse internally and form strong adhesion between one another after contact (properties not seen in a purely mono-valent environment).

  9. Studying Intermolecular Forces with a Dual Gas Chromatography and Boiling Point Investigation

    Cunningham, William Patrick; Xia, Ian; Wickline, Kaitlyn; Huitron, Eric Ivan Garcia; Heo, Jun

    2018-01-01

    A procedure for the study of structural differences and intermolecular attraction between ethanol and 1-butanol based in laboratory work is described. This study provides comparisons of data retrieved from both a determination of boiling point and gas chromatography traces for the mixture. The methodology reported here should provide instructors…

  10. Intermolecular spectroscopy

    Gelbart, W.M.

    1980-01-01

    In this article some of the theoretical background is presented for the following papers on 'Intermolecular Spectroscopy and Dynamical Properties of Dense Systems'. In Section 1 we outline a simple semi-classical description of the interaction between optical radiation and matter. The motion of a many-body polarizability is introduced; limiting forms of this complicated quantity lead to the familiar cases of light scattering spectra. In Section 2 we consider the linear response approximation, and the equation of motion for the many-body density matrix is solved to first order in the matter-radiation interaction. The often quoted fluctuation-dissipation theorem and the time-dependent, equilibrium correlation functions are discussed. Section 3 treats the problem of the local field. In Section 4 we consider the special case of collision-induced light scattering by atomic fluids in the low-density limit. This allows us to focus on determining the interaction polarizability for simple gases. Finally, in Section 5 we distinguish between collision-induced and multiple light scattering, and discuss the double-light-scattering analyses which provide new information about critical and thermodynamically unstable fluids. (KBE)

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

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

    2016-05-01

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

  12. Catalyst-Controlled and Tunable, Chemoselective Silver-Catalyzed Intermolecular Nitrene Transfer: Experimental and Computational Studies.

    Dolan, Nicholas S; Scamp, Ryan J; Yang, Tzuhsiung; Berry, John F; Schomaker, Jennifer M

    2016-11-09

    The development of new catalysts for selective nitrene transfer is a continuing area of interest. In particular, the ability to control the chemoselectivity of intermolecular reactions in the presence of multiple reactive sites has been a long-standing challenge in the field. In this paper, we demonstrate examples of silver-catalyzed, nondirected, intermolecular nitrene transfer reactions that are both chemoselective and flexible for aziridination or C-H insertion, depending on the choice of ligand. Experimental probes present a puzzling picture of the mechanistic details of the pathways mediated by [( t Bu 3 tpy)AgOTf] 2 and (tpa)AgOTf. Computational studies elucidate these subtleties and provide guidance for the future development of new catalysts exhibiting improved tunability in group transfer reactions.

  13. Intermolecular interactions

    Kaplan, I.G.; Rodimova, O.B.; AN SSSR, Tomsk. Inst. Optiki Atmosfery)

    1978-01-01

    The present state of the intermolecular interaction theory is described. The general physical picture of the molecular interactions is given, the relative contributions of interactions of different types are analyzed (electrostatic, resonance, induction, dispersion, relativistic, magnetostatic and exchange), and the main ones in each range of separations are picked out. The methods of the potential curve calculations are considered, specific for definite separations between the interacting systems. The special attention is paid to the analysis of approximations used in different theoretical calculation methods

  14. Systematic study on intermolecular valence-band dispersion in molecular crystalline films

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2015-01-01

    Highlights: • Intermolecular valence-band dispersion of crystalline films of phthalocyanines. • Intermolecular transfer integral versus lattice constant. • Site-specific intermolecular interaction and resultant valence-band dispersion. • Band narrowing effect induced by elevated temperature. - Abstract: Functionalities of organic semiconductors are governed not only by individual properties of constituent molecules but also by solid-state electronic states near the Fermi level such as frontier molecular orbitals, depending on weak intermolecular interactions in various conformations. The individual molecular property has been widely investigated in detail; on the other hand, the weak intermolecular interaction is difficult to investigate precisely due to the presence of the structural and thermal energy broadenings in organic solids. Here we show quite small but essential intermolecular valence band dispersions and their temperature dependence of sub-0.1-eV scale in crystalline films of metal phthalocyanines (H_2Pc, ZnPc, CoPc, MnPc, and F_1_6ZnPc) by using angle-resolved photoemission spectroscopy (ARPES) with synchrotron radiation. The observed bands show intermolecular and site dependent dispersion widths, phases, and periodicities, for different chemical substitution of terminal groups and central metals in the phthalocyanine molecule. The precise and systematic band-dispersion measurement would be a credible approach toward the comprehensive understanding of intermolecular interactions and resultant charge transport properties as well as their tuning by substituents in organic molecular systems.

  15. INS study of intermolecular interaction at the silicone-fumed silica interface

    Sheka, E.F.; Natkaniec, I.

    1999-01-01

    Complete text of publication follows. The paper presents results related to the interface formed between finned silica particles and polydimethylsiloxane polymers, presented in the study by a five-member cyclic oligomer SiS. The substrate surface is terminated by either hydroxyl units or by trimethylsiloxy ones. When the interface is formed, methyl units are the main constituents providing neutron scattering. Protium/deuterium exchange has been used to distinguish the latter belonging to either adsorbate or substrate. A detailed analysis of the intermolecular interaction impact on both adsorbed molecule and substrate has been performed. The observed features are supported by the vibrational spectra calculations performed on the basis of a modem quantum-chemical approach and supplemented by the solution of the inverse spectral problem. (author)

  16. Chain-length-dependent intermolecular packing in polyphenylenes: a high pressure study

    Heimel, G; Oehzelt, M; Hummer, K; Koppelhuber-Bitschnau, B; Porsch, F; Ambrosch-Draxl, C; Resel, R

    2003-01-01

    We report on pressure-induced structural changes in crystalline oligo(para-phenylenes) containing two to six phenyl rings. The results are discussed with particular emphasis put on the implications these changes in intermolecular distances and molecular arrangement have on important bulk properties of this class of materials, such as optical response and charge transport. We performed energy dispersive x-ray diffraction in a systematic study on polycrystalline powders of biphenyl, para-terphenyl, p-quaterphenyl, p-quinquephenyl and p-sexiphenyl under hydrostatic pressure up to 60 kbar. Revisiting the crystal structures at ambient conditions reveals details in the packing principle. A linear relationship between the density at ambient conditions and the number of phenyl rings is found. High pressure data not only yields pressure-dependent lattice parameters and hints towards pressure-induced changes in the molecular arrangement but also allows for an analysis of the equations of state of these substances as a ...

  17. Effect of intermolecular force on the static/dynamic behaviour of M/NEM devices

    Kim, Namjung; Aluru, N. R.

    2014-12-01

    Advances made in the fabrication of micro/nano-electromechanical (M/NEM) devices over the last ten years necessitate the understanding of the attractive force that arises from quantum fluctuations (generally referred to as Casimir effects) [Casimir H B G 1948 Proc. K. Ned. Akad. Wet. 51 793]. The fundamental mechanisms underlying quantum fluctuations have been actively investigated through various theoretical and experimental approaches. However, the effect of the force on M/NEM devices has not been fully understood yet, especially in the transition region involving gaps ranging from 10 nm to 1 μm, due to the complexity of the force. Here, we numerically calculate the Casimir effects in M/NEM devices by using the Lifshitz formula, the general expression for the Casimir effects [Lifshitz E 1956 Sov. Phys. JETP 2 73]. Since the Casimir effects are highly dependent on the permittivity of the materials, the Kramer-Kronig relation [Landau L D, Lifshitz E M and Pitaevskii L P 1984 Electrodynamics of Continuous Media (New York: Pergamon Press)] and the optical data for metals and dielectrics are used in order to obtain the permittivity. Several simplified models for the permittivity of the materials, such as the Drude and Lorentz models [Jackson J D 1975 Classical Electrodynamics (New York: Wiley)], are also used to extrapolate the optical data. Important characteristic values of M/NEM devices, such as the pull-in voltage, pull-in gap, detachment length, etc, are calculated for devices operating in the transition region. Our results show that accurate predictions for the pull-in behaviour are possible when the Lifshitz formula is used instead of the idealized expressions for Casimir effects. We expand this study into the dynamics of M/NEM devices, so that the time and frequency response of M/NEM devices with Casimir effects can be explored.

  18. Effect of intermolecular force on the static/dynamic behaviour of M/NEM devices

    Kim, Namjung; Aluru, N R

    2014-01-01

    Advances made in the fabrication of micro/nano-electromechanical (M/NEM) devices over the last ten years necessitate the understanding of the attractive force that arises from quantum fluctuations (generally referred to as Casimir effects) [Casimir H B G 1948 Proc. K. Ned. Akad. Wet. 51 793]. The fundamental mechanisms underlying quantum fluctuations have been actively investigated through various theoretical and experimental approaches. However, the effect of the force on M/NEM devices has not been fully understood yet, especially in the transition region involving gaps ranging from 10 nm to 1 μm, due to the complexity of the force. Here, we numerically calculate the Casimir effects in M/NEM devices by using the Lifshitz formula, the general expression for the Casimir effects [Lifshitz E 1956 Sov. Phys. JETP 2 73]. Since the Casimir effects are highly dependent on the permittivity of the materials, the Kramer–Kronig relation [Landau L D, Lifshitz E M and Pitaevskii L P 1984 Electrodynamics of Continuous Media (New York: Pergamon Press)] and the optical data for metals and dielectrics are used in order to obtain the permittivity. Several simplified models for the permittivity of the materials, such as the Drude and Lorentz models [Jackson J D 1975 Classical Electrodynamics (New York: Wiley)], are also used to extrapolate the optical data. Important characteristic values of M/NEM devices, such as the pull-in voltage, pull-in gap, detachment length, etc, are calculated for devices operating in the transition region. Our results show that accurate predictions for the pull-in behaviour are possible when the Lifshitz formula is used instead of the idealized expressions for Casimir effects. We expand this study into the dynamics of M/NEM devices, so that the time and frequency response of M/NEM devices with Casimir effects can be explored. (paper)

  19. Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.

    Zheng-Yu Jiang

    Full Text Available Degradation of certain proteins through the ubiquitin-proteasome pathway is a common strategy taken by the key modulators responsible for stress responses. Kelch-like ECH-associated protein-1(Keap1, a substrate adaptor component of the Cullin3 (Cul3-based ubiquitin E3 ligase complex, mediates the ubiquitination of two key modulators, NF-E2-related factor 2 (Nrf2 and IκB kinase β (IKKβ, which are involved in the redox control of gene transcription. However, compared to the Keap1-Nrf2 protein-protein interaction (PPI, the intermolecular recognition mechanism of Keap1 and IKKβ has been poorly investigated. In order to explore the binding pattern between Keap1 and IKKβ, the PPI model of Keap1 and IKKβ was investigated. The structure of human IKKβ was constructed by means of the homology modeling method and using reported crystal structure of Xenopus laevis IKKβ as the template. A protein-protein docking method was applied to develop the Keap1-IKKβ complex model. After the refinement and visual analysis of docked proteins, the chosen pose was further optimized through molecular dynamics simulations. The resulting structure was utilized to conduct the virtual alanine mutation for the exploration of hot-spots significant for the intermolecular interaction. Overall, our results provided structural insights into the PPI model of Keap1-IKKβ and suggest that the substrate specificity of Keap1 depend on the interaction with the key tyrosines, namely Tyr525, Tyr574 and Tyr334. The study presented in the current project may be useful to design molecules that selectively modulate Keap1. The selective recognition mechanism of Keap1 with IKKβ or Nrf2 will be helpful to further know the crosstalk between NF-κB and Nrf2 signaling.

  20. The study of intermolecular interactions in NLO crystal melaminium chloride hemihydrate using DFT simulation and Hirshfeld surface analysis

    Sangeetha, K.; Kumar, V. R. Suresh; Marchewka, M. K.; Binoy, J.

    2018-05-01

    Since, the intermolecular interactions play a crucial role in the formation of crystalline network, its analysis throws light on structure dependent crystalline properties. In the present study, DFT based vibrational spectral investigation has been performed in the stretching region (3500 cm-1 - 2800 cm-1) of IR and Raman spectra of melaminium chloride hemihydrates. The intermolecular interaction has been investigated by analyzing the half width of the OH and NH stretching profile of the deconvoluted spectra. Correlation of vibrational spectra with Hirshfeld surface analysis and finger print plot has been contemplated and molecular docking studies has been performed on melaminium chloride hemihydrate to assess its role in the drug transport mechanism and toxicity to human body.

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

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

    2014-10-07

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

  2. ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

    Sengul, Mert Y.; Randall, Clive A.; van Duin, Adri C. T.

    2018-04-01

    The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ xHAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ xHAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

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

    Heßelmann, Andreas; Korona, Tatiana

    2014-01-01

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

  4. MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

    Abdel-Azeim, Safwat

    2014-05-06

    Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

  5. Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

    Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

    2017-04-01

    DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

  6. Study of intermolecular interactions in binary mixtures of 2-(dimethylamino)ethanol with methanol and ethanol at various temperatures

    Pandey, Puneet Kumar; Pandey, Vrijesh Kumar; Awasthi, Anjali; Nain, Anil Kumar; Awasthi, Aashees

    2014-01-01

    Graphical abstract: The densities and ultrasonic speeds of the binary mixtures over the entire composition range were measured at various temperatures at atmospheric pressure. The excess molar volumes, isentropic compressibilities, and molar isentropic compressions have been calculated. The variations of these parameters with composition and temperature are discussed. The IR spectra were recorded they further supported the conclusion drawn from excess parameters, which indicates the presence of intermolecular hydrogen bonding between the oxygen atom of DMAE molecules and hydrogen atom of methanol and ethanol molecules in these mixtures.. - Highlights: • The study reports density and ultrasonic velocity data of 2-(dimethylamino)ethanol + methanol/ethanol mixtures. • To elucidate the interactions in 2-(dimethylamino)ethanol + methanol/ethanol binary mixtures. • Provides information on nature and relative strength of interactions in these mixtures. • Correlates physicochemical properties with interactions in these mixtures. - Abstract: The densities, ρ and ultrasonic speeds, u of the binary mixtures of 2-(dimethylamino)ethanol (DMAE) with methanol/ethanol, including those of pure liquids, over the entire composition range were measured at 298.15, 308.15 and 318.15 K. From the experimental data, the excess molar volumes, V m E and excess isentropic compressibilities, κ s E have been calculated. The excess partial molar volumes, V ¯ m,1 E and V ¯ m,2 E and excess partial molar isentropic compressions, K ¯ s,m,1 E and K ¯ s,m,2 E over the whole composition range; and partial molar volumes, V ¯ m,1 ° and V ¯ m,2 ° , partial molar isentropic compressions, K ¯ s,m,1 ° and K ¯ s,m,2 ° , excess partial molar volumes, V ¯ m,1 °E and V ¯ m,2 °E , and excess partial molar isentropic compressions, K ¯ s,m,1 °E and K ¯ s,m,2 °E at infinite dilution have also been calculated. The variations of these parameters with composition and temperature are

  7. A Raman spectroscopy study on the effects of intermolecular hydrogen bonding on water molecules absorbed by borosilicate glass surface

    Li, Fabing; Li, Zhanlong; Wang, Ying; Wang, Shenghan; Wang, Xiaojun; Sun, Chenglin; Men, Zhiwei

    2018-05-01

    The structural forms of water/deuterated water molecules located on the surface of borosilicate capillaries have been first investigated in this study on the basis of the Raman spectral data obtained at different temperatures and under atmospheric pressure for molecules in bulk and also for molecules absorbed by borosilicate glass surface. The strongest two fundamental bands locating at 3063 cm-1 (2438 cm-1) in the recorded Raman spectra are assigned here to the Osbnd H (Osbnd D) bond stretching vibrations and they are compared with the corresponding bands observed at 3124 cm-1 (2325 cm-1) in the Raman spectrum of ice Ih. Our spectroscopic observations have indicated that the structure of water and deuterated water molecules on borosilicate surface is similar to that of ice Ih (hexagonal phase of ice). These observations have also indicated that water molecules locate on the borosilicate surface so as to construct a bilayer structure and that strong and weak intermolecular hydrogen bonds are formed between water/deuterated molecules and silanol groups on borosilicate surface. In accordance with these findings, water and deuterated water molecules at the interface of capillary have a higher melting temperature.

  8. Intermolecular and surface forces

    Israelachvili, Jacob N

    2011-01-01

    This reference describes the role of various intermolecular and interparticle forces in determining the properties of simple systems such as gases, liquids and solids, with a special focus on more complex colloidal, polymeric and biological systems. The book provides a thorough foundation in theories and concepts of intermolecular forces, allowing researchers and students to recognize which forces are important in any particular system, as well as how to control these forces. This third edition is expanded into three sections and contains five new chapters over the previous edition.· starts fr

  9. Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components

    Makarewicz, Jan, E-mail: jama@amu.edu.pl; Shirkov, Leonid [Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań (Poland)

    2016-05-28

    The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy D{sub e} of 392 cm{sup −1} is close to that of 387 cm{sup −1} calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, D{sub e} for PAr becomes slightly lower than D{sub e} for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

  10. Iodine bonding stabilizes iodomethane in MIDAS pesticide. Theoretical study of intermolecular interactions between iodomethane and chloropicrin.

    Glaser, Rainer; Prugger, Kaitlan

    2012-02-22

    The results are reported of a theoretical study of iodomethane (H(3)C-I, 1) and chloropicrin (Cl(3)C-NO(2), 2), of the heterodimers 3-6 formed by aggregation of 1 and 2, and of their addition products 7 and 8 and their possible fragmentation reactions to 9-18. Mixtures of iodomethane and chloropicrin are not expected to show chemistry resulting from their reactions with each other. The structures and stabilities are discussed of the iodine-bonded molecular aggregates (IBMA) 3 and 4 and of the hydrogen- and iodine-bonded molecular aggregates (IHBMA) 5 and 6. The mixed aggregates 3-5 are bound on the free enthalpy surface relative to the homodimers of 1 and 2, and the IBMA structures 3 and 4 are most stable. This result suggests that the mixture of chloropicrin and iodomethane in the pesticide Midas is a good choice to reduce the volatility of iodomethane because of thermodynamically stabilizing iodine bonding.

  11. Intermolecular interactions in mixtures of poly (ethylene glycol) with methoxybenzene and ethoxybenzene: Volumetric and viscometric studies

    Zafarani-Moattar, Mohammed Taghi; Dehghanian, Saeedeh

    2014-01-01

    Highlights: • Density and viscosity values of PEG400 + methoxybenzene or + ethoxybenzene were measured. • The excess molar volume and thermodynamic functions of activation were calculated. • The results were interpreted in light of polymer–solvent interactions. • The changes in activation function indicate the viscous flow process. • The thermodynamic functions were correlated with the suitable equations. -- Abstract: The density and viscosity values of the binary mixtures of {poly (ethylene glycol) (PEG400) + methoxybenzene, or + ethoxybenzene} have been measured at T = (298.15, 308.15, and 318.15) K. From these experimental values, the excess molar volume, apparent specific volume, partial specific volume of solute, partial specific volume of solvent and excess Gibbs free energy of activation have been computed over the entire range of composition at three temperatures. From the experimental data, the thermodynamic functions of activation have been estimated for each binary mixture. The obtained results have been interpreted in light of polymer–solvent interactions and packing effects. The signs of excess molar volume and deviations of excess Gibbs free energy of activation have been used to obtain some information in regard to existence of specific interactions between PEG400 and solvents molecules. The changes in entropy and enthalpy of activation from the initial state to the transition state were also calculated in order to see which one of these functions controls viscous flow process in the studied polymer solutions. The excess molar volume and excess Gibbs free energy of activation values have been adequately fitted to the Redlich–Kister polynomial. Apparent specific volume values were correlated with the suitable equation. The different models proposed for correlating the viscosity of polymer solutions or liquid mixtures (segment-based-Eyring–NRTL, segment-based-Eyring–Wilson, Grunbreg–Nissan, Frenkel, Hind et al., Katti

  12. Mechanism of intermolecular hydroacylation of vinylsilanes catalyzed by a rhodium(I) olefin complex: a DFT study.

    Meng, Qingxi; Shen, Wei; Li, Ming

    2012-03-01

    Density functional theory (DFT) was used to investigate the Rh(I)-catalyzed intermolecular hydroacylation of vinylsilane with benzaldehyde. All intermediates and transition states were optimized completely at the B3LYP/6-31G(d,p) level (LANL2DZ(f) for Rh). Calculations indicated that Rh(I)-catalyzed intermolecular hydroacylation is exergonic, and the total free energy released is -110 kJ mol(-1). Rh(I)-catalyzed intermolecular hydroacylation mainly involves the active catalyst CA2, rhodium-alkene-benzaldehyde complex M1, rhodium-alkene-hydrogen-acyl complex M2, rhodium-alkyl-acyl complex M3, rhodium-alkyl-carbonyl-phenyl complex M4, rhodium-acyl-phenyl complex M5, and rhodium-ketone complex M6. The reaction pathway CA2 + R2 → M1b → T1b → M2b → T2b1 → M3b1 → T4b → M4b → T5b → M5b → T6b → M6b → P2 is the most favorable among all reaction channels of Rh(I)-catalyzed intermolecular hydroacylation. The reductive elimination reaction is the rate-determining step for this pathway, and the dominant product predicted theoretically is the linear ketone, which is consistent with Brookhart's experiments. Solvation has a significant effect, and it greatly decreases the free energies of all species. The use of the ligand Cp' (Cp' = C(5)Me(4)CF(3)) decreased the free energies in general, and in this case the rate-determining step was again the reductive elimination reaction.

  13. Theoretical studies for the N2–N2O van der Waals complex: The potential energy surface, intermolecular vibrations, and rotational transition frequencies

    Zheng, Rui; Zheng, Limin; Yang, Minghui; Lu, Yunpeng

    2015-01-01

    Theoretical studies of the potential energy surface (PES) and bound states are performed for the N 2 –N 2 O van der Waals (vdW) complex. A four-dimensional intermolecular PES is constructed at the level of single and double excitation coupled-cluster method with a non-iterative perturbation treatment of triple excitations [CCSD(T)] with aug-cc-pVTZ basis set supplemented with bond functions. Two equivalent T-shaped global minima are located, in which the O atom of N 2 O monomer is near the N 2 monomer. The intermolecular fundamental vibrational states are assigned by inspecting the orientation of the nodal surface of the wavefunctions. The calculated frequency for intermolecular disrotation mode is 23.086 cm −1 , which is in good agreement with the available experimental data of 22.334 cm −1 . A negligible tunneling splitting with the value of 4.2 MHz is determined for the ground vibrational state and the tunneling splitting increases as the increment of the vibrational frequencies. Rotational levels and transition frequencies are calculated for both isotopomers 14 N 2 –N 2 O and 15 N 2 –N 2 O. The accuracy of the PES is validated by the good agreement between theoretical and experimental results for the transition frequencies and spectroscopic parameters

  14. Combining an Elastic Network With a Coarse-Grained Molecular Force Field : Structure, Dynamics, and Intermolecular Recognition

    Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.

    Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this

  15. Determination of intermolecular transfer integrals from DFT calculations

    Baumeier, Bjoern; Andrienko, Denis [Max-Planck Institute for Polymer Research, Mainz (Germany)

    2010-07-01

    Theoretical studies of charge transport in organic conducting systems pose a unique challenge since they require multiscale schemes that combine quantum-chemical, molecular dynamics and kinetic Monte-Carlo calculations. The description of the mobility of electrons and holes in the hopping regime relies on the determination of intermolecular hopping rates in large scale morphologies. Using Marcus theory these rates can be calculated from intermolecular transfer integrals and on-site energies. Here we present a detailed computational study on the accuracy and efficiency of density-functional theory based approaches to the determination of intermolecular transfer integrals. First, it is demonstrated how these can be obtained from quantum-chemistry calculations by forming the expectation value of a dimer Fock operator with frontier orbitals of two neighboring monomers based on a projective approach. We then consider the prototypical example of one pair out of a larger morphology of Tris(8-hydroxyquinolinato)aluminium (Alq3) and study the influence of computational parameters, e.g. the choice of basis sets, exchange-correlation functional, and convergence criteria, on the calculated transfer integrals. The respective accuracies and efficiencies are compared in order to derive an optimal strategy for future simulations based on the full morphology.

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

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

    2006-08-01

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

  17. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    Peter I. Nagy

    2014-10-01

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

  18. Synthesis and studies on structural, optical and nonlinear optical properties of novel organic inter-molecular compounds: 4-chloro-3-nitroaniline-3-hydroxy benzaldehyde and urea-4-dimethylaminopyridine

    Pandey, Priyanka; Rai, R. N.

    2018-05-01

    Two novel organic inter-molecular compounds (IMCs), (3-(4-chloro-3-nitrophenylimino) methyl) phenol) (CNMP) and urea ̶ 4-dimethylaminopyridine complex (UDMAP), have been synthesized by solid state reaction. These two IMCs were identified by phase diagram study of CNA-HB and U-DMAP systems. The single crystals of newly obtained IMCs were grown by slow solvent evaporation technique at room temperature. Both the IMCs were further studied for their thermal, spectral, single crystal XRD for their atomic packing in molecule, crystallinity, optical and nonlinear optical behaviour. In both the cases, melting point of inter-molecular compounds was found to be higher than that of their parent components, CNMP was found to be thermally stable up to 158 °C while UDMAP was stable up to 144 °C, which indicate their extra stability than their parents. The single crystal XRD studies confirmed that CNMP has crystallized in orthorhombic unit cell with non-centrosymmetric space group P212121 while UDMAP has crystallized in monoclinic unit cell with centrosymmetric space group C2/c. The absorption spectrum of CNMP was found to be in between the absorption of parents, while broadening of peak and red shift was observed in UDMAP as compared to the parents. Second order nonlinear optical property of CNMP and UDMAP was studied using Kurtz Perry powder technique and intense green light emission was observed with CNMP on excitation with 1064 nm of Nd:YAG laser while no emission was observed with UDMAP.

  19. Desensitization of metastable intermolecular composites

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

    2011-04-26

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

  20. Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

    Jee, Jun Goo

    2010-01-01

    It has been shown that AMD refinement is very useful for defining an intermolecular hydrogen bond in NMR structure calculation. The refined structure also provides a clue for explaining the pH dependence in Ub and UIM complexes. As reported by Choi et al., serine-mediated hydrogen bonds are the third most populated hydrogen bonds found in protein-protein intermolecular interactions, after the backbone-backbone and backbone-aspartate ones. The abundance imposes the requirement of an method to determine the interface of protein-protein complexes. The precise geometry is particularly important in the complex structures between Ub and UBDs. Ub recognizes various targets with the same surface, where both hydrophobic and hydrophobic interactions are involved. Hence, the details of the hydrophilic interactions are necessary to find the common binding modes. The structure determination of a biomolecule by NMR depends heavily on the distance restraints derived by the NOE cross peaks that are observed between two protons within 6 A through space. Therefore, the existence of the NOE peaks and their correct assignments to two corresponding protons are essential for an accurate and precise structure determination. Recent developments of NOE assignment and calculation algorithms have enabled the determination of protein 3D structures without any manual interpretation, provided chemical shifts are assigned in most atoms and sufficient NOE peaks exist. Along with these advances, the necessity of determining complicated structures such as complexes is increasing

  1. Competing intermolecular interactions of artemisinin-type agents and aspirin with membrane phospholipids: Combined model mass spectrometry and quantum-chemical study

    Pashynska, Vlada, E-mail: vlada@vl.kharkov.ua [B.Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, Lenin Ave., 47, 61103 Kharkov (Ukraine); Stepanian, Stepan [B.Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, Lenin Ave., 47, 61103 Kharkov (Ukraine); Gömöry, Agnes; Vekey, Karoly [Institute of Organic Chemistry of Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Magyar tudosok korutja, 2, Budapest H-1117 (Hungary); Adamowicz, Ludwik [University of Arizona, Department of Chemistry and Biochemistry, Tucson, AZ 85721 (United States)

    2015-07-09

    Highlights: • Competitive binding of artemisinin agents and aspirin with phospholipids is shown. • Complexation between the antimalarial drugs and aspirin molecules is also found. • Energetically favorable structures of the model complexes are identified by DFT. • Membranotropic activity of the studied drugs can be modified under joint usage. - Abstract: Study of intermolecular interactions of antimalarial artemisinin-type drugs and aspirin with membrane phospholipids is important in term of elucidation of the drugs activity modification under their joint usage. Combined experimental and computational study of the interaction of dihydroartemisinin, α-artemether, and artesunate with aspirin (ASP) and dipalmitoylphosphatidylcholine (DPPC) is performed by electrospray ionization (ESI) mass spectrometry and by DFT B3LYP/aug-cc-pVDZ methods. The results of the ESI investigation of systems containing artemisinin-type agent, ASP and DPPC, reveal a competition between the antimalarial agents and ASP for binding with DPPC molecules. The complexation between the antimalarial drugs and ASP is also found. Observed phenomena suggest that membranotropic activity of artemisin-type agents and aspirin is modified under their combined usage. To elucidate structure-energy characteristics of the non-covalent complexes studied the model DFT calculations are performed for dihydroartemisinin · ASP complex and complexes of the each drug with phosphatidylcholine head of DPPC in neutral and cationized forms.

  2. Competing intermolecular interactions of artemisinin-type agents and aspirin with membrane phospholipids: Combined model mass spectrometry and quantum-chemical study

    Pashynska, Vlada; Stepanian, Stepan; Gömöry, Agnes; Vekey, Karoly; Adamowicz, Ludwik

    2015-01-01

    Highlights: • Competitive binding of artemisinin agents and aspirin with phospholipids is shown. • Complexation between the antimalarial drugs and aspirin molecules is also found. • Energetically favorable structures of the model complexes are identified by DFT. • Membranotropic activity of the studied drugs can be modified under joint usage. - Abstract: Study of intermolecular interactions of antimalarial artemisinin-type drugs and aspirin with membrane phospholipids is important in term of elucidation of the drugs activity modification under their joint usage. Combined experimental and computational study of the interaction of dihydroartemisinin, α-artemether, and artesunate with aspirin (ASP) and dipalmitoylphosphatidylcholine (DPPC) is performed by electrospray ionization (ESI) mass spectrometry and by DFT B3LYP/aug-cc-pVDZ methods. The results of the ESI investigation of systems containing artemisinin-type agent, ASP and DPPC, reveal a competition between the antimalarial agents and ASP for binding with DPPC molecules. The complexation between the antimalarial drugs and ASP is also found. Observed phenomena suggest that membranotropic activity of artemisin-type agents and aspirin is modified under their combined usage. To elucidate structure-energy characteristics of the non-covalent complexes studied the model DFT calculations are performed for dihydroartemisinin · ASP complex and complexes of the each drug with phosphatidylcholine head of DPPC in neutral and cationized forms

  3. Solvation study of the non-specific lipid transfer protein from wheat by intermolecular NOEs with water and small organic molecules

    Liepinsh, Edvards; Sodano, Patrick; Tassin, Severine; Marion, Didier; Vovelle, Francoise; Otting, Gottfried

    1999-01-01

    Intermolecular nuclear Overhauser effects (NOEs) were measured between the protons of various small solvent or gas molecules and the non-specific lipid transfer protein (ns-LTP) from wheat. Intermolecular NOEs were observed with the hydrophobic pocket in the interior of wheat ns-LTP, which grew in intensity in the order cyclopropane (saturated solution) < methane (140 bar) < ethane (40 bar) < acetonitrile (5% in water) < cyclohexane (saturated solution) < benzene (saturated solution). No intermolecular NOEs were observed with dioxane (5% in water). The intermolecular NOEs were negative for all of the organic molecules tested. Intermolecular NOEs between wheat ns-LTP and water were weak or could not be distinguished from exchange-relayed NOEs. As illustrated by the NOEs with cyclohexane versus dioxane, the hydrophobic pocket in wheat ns-LTP preferably binds non-polar molecules. Yet, polar molecules like acetonitrile can also be accommodated. The pressure dependence of the NOEs between methane and wheat ns-LTP indicated incomplete occupancy, even at 190 bar methane pressure. In general, NOE intensities increased with the size of the ligand molecule and its vapor pressure. NMR of the vapor phase showed excellent resolution between the signals from the gas phase and those from the liquid phase. The vapor concentration of cyclohexane was fivefold higher than that of the dioxane solution, supporting the binding of cyclohexane versus uptake of dioxane

  4. Green synthesis, characterization and some physico-chemical studies on a novel intermolecular compound; 4-nitro-o-phenylenediamine-N, N-dimethylaminobenzaldehyde system

    Rai, U. S.; Singh, Manjeet; Rai, R. N.

    2017-09-01

    An inter-molecular compound (IMC) L1 was synthesized by taking 1:1 molar ratio of p-nitro-o-phenylenediamine (NOPDA) and N, N-dimethylaminobenzaldehyde (DMAB) via thermally initiated solid state reaction. It was characterized by X-ray diffraction, spectral and optical studies. The single crystal of the (L1) was grown from saturated solution of ethanol using slow evaporation technique at 29 °C. From the single crystal X-ray diffraction analysis, it can be inferred that it crystallizes in triclinic unit cell with P-1 space group (CCDC No 1422765). Absorption spectrum of IMC (L1) shows a band at 318 nm attributed to the intra-molecular charge-transfer (ICT) excited state absorption and the other band at 376 nm is due to n→π* transition. The IMC (L1) shows a strong fluorescence at 418 nm with a Stokes shift (≈100 nm) and quantum efficiency (0.22) upon excitation in methyl alcohol at 318 nm.

  5. Intra- and inter-molecular energy transfer studies. Progress report, 1 June 1974--31 May 1975

    Nicol, M.F.

    1975-01-01

    The analysis of pressure-induced effects on the intersystem crossing in anthracene; determination of the influence of hydrogen-bonding on the intersystem crossing rate and phosphorescence of azines; experimental studies of the kinetics of high-pressure structural transitions in Teflon; testing of liquid helium temperature high-pressure optical cells; excimer production in compound crystalline aromatic hydrocarbons; and studies of the structure and chemistry of dianthracene at high pressures are described. (6 figs.) (GHT)

  6. Electronic transitions and intermolecular forces

    Hemert, M.C. van.

    1981-01-01

    This thesis describes two different subjects - electronic transitions and intermolecular forces - that are related mainly by the following observation: The wavenumber at which an electronic transition in an atom or molecule occurs, depends on the environment of that atom or molecule. This implies, for instance, that when a molecule becomes solvated its absorption spectrum may be shifted either to the blue or to the red side of the original gasphase spectrum. In part I attention is paid to the experimental aspects of VUV spectroscopy, both in the gasphase and in the condensed phase. In part II a series of papers are presented, dealing with the calculation of intermolecular forces (and some related topics) both for the ground state and for the excited state interactions, using different non-empirical methods. The calculations provide, among other results, a semiquantitative interpretation of the spectral blue shifts encountered in our experiments. (Auth.)

  7. Combined experimental and theoretical study of the mechanism and enantioselectivity of palladium-catalyzed intermolecular Heck coupling

    Henriksen, Signe Teuber; Norrby, Per-Ola; Kaukoranta, Päivi

    2008-01-01

    . The steric interactions in this transition state fully account for the enantioselectivity observed with the ligands studied. The calculations also predict relative reactivity and nonlinear mixing effects for the investigated ligands; these predictions are fully validated by experimental testing. Finally......The asymmetric Heck reaction using P,N-ligands has been studied by a combination of theoretical and experimental methods. The reaction follows Halpern-style selectivity; that is, the major isomer is produced from the least favored form of the pre-insertion intermediate. The initially formed Ph......, the low conversion observed with some catalysts was found to be caused by inactivation due to weak binding of the ligand to Pd(0). Adding monodentate PPh3 alleviated the precipitation problem without deteriorating the enantioselectivity and led to one of the most effective catalytic systems to date....

  8. Microassembly by intermolecular forces

    Henderson, S.J.; White, J.W.

    1988-01-01

    The value of neutron and X-ray small-angle scattering for studying self assembly of molecular-sized units into interesting chemical and electrical structures is illustrated with three different types of system. The amphiphilic nature of a polyacetylene-polyisoprene [(CH) x PI] AB block copolymer and some of the structure arising from this are seen in neutron scattering from (CD) x PI solids and solutions. The action of template molecules in zeolite synthesis is discussed and template action of the tetrapropylammonium ion at room temperature in soluble silicate gels demonstrated. Finally, very large interplatelet spacings in clay sols are recorded using small-angle X-ray scattering and the swelling behaviour of these systems is characterized. Their usefulness for pillared clay synthesis is discussed. (orig.)

  9. Molecular dynamics-assisted pharmacophore modeling of caspase-3-isatin sulfonamide complex: Recognizing essential intermolecular contacts and features of sulfonamide inhibitor class for caspase-3 binding.

    Kumar, Sivakumar Prasanth; Patel, Chirag N; Jha, Prakash C; Pandya, Himanshu A

    2017-12-01

    The identification of isatin sulfonamide as a potent small molecule inhibitor of caspase-3 had fuelled the synthesis and characterization of the numerous sulfonamide class of inhibitors to optimize for potency. Recent works that relied on the ligand-based approaches have successfully shown the regions of optimizations for sulfonamide scaffold. We present here molecular dynamics-based pharmacophore modeling of caspase-3-isatin sulfonamide crystal structure, to elucidate the essential non-covalent contacts and its associated pharmacophore features necessary to ensure caspase-3 optimal binding. We performed 20ns long dynamics of this crystal structure to extract global conformation states and converted into structure-based pharmacophore hypotheses which were rigorously validated using an exclusive focussed library of experimental actives and inactives of sulfonamide class by Receiver Operating Characteristic (ROC) statistic. Eighteen structure-based pharmacophore hypotheses with better sensitivity and specificity measures (>0.6) were chosen which collectively showed the role of pocket residues viz. Cys163 (S 1 sub-site; required for covalent and H bonding with Michael acceptor of inhibitors), His121 (S 1 ; π stack with bicyclic isatin moiety), Gly122 (S 1 ; H bond with carbonyl oxygen) and Tyr204 (S 2 ; π stack with phenyl group of the isatin sulfonamide molecule) as stringent binding entities for enabling caspase-3 optimal binding. The introduction of spatial pharmacophore site points obtained from dynamics-based pharmacophore models in a virtual screening strategy will be helpful to screen and optimize molecules belonging to sulfonamide class of caspase-3 inhibitors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. The Effect of Intermolecular Halogen Bond on 19F DNP Enhancement in 1, 4-Diiodotetrafluorobenzene/4-OH-TEMPO Supramolecular Assembly

    GAO Shan

    2017-12-01

    Full Text Available Halogen bond, as hydrogen bond, is a non-covalent bond. Dynamic nuclear polarization (DNP technique has been used previously to study hydrogen bonds-mediated intermolecular interactions. However, no study has been carried out so far to study the halogen bond-mediated intermolecular interactions with DNP. In this work, 19F DNP polarization efficiency of the halogen bonds existing in supramolecular assembling by 4-OH-TEMPO and 1,4-diiodotetrafluorobenzene (DITFB was studied on a home-made DNP system. The formation of intermolecular halogen bonds appeared to increase 19F DNP polarization efficiency, suggesting that the spin-spin interactions among electrons were weakened by the halogen bonds, resulting in an increased T2e and a larger saturation factor.

  11. Modulation of intermolecular interactions in single-molecule magnets

    Heroux, Katie Jeanne

    Polynuclear manganese clusters exhibiting interesting magnetic and quantum properties have been an area of intense research since the discovery of the first single-molecule magnet (SMM) in 1993. These molecules, below their blocking temperature, function as single-domain magnetic particles which exhibit classical macroscale magnetic properties as well as quantum mechanical phenomena such as quantum tunnelling of magnetization (QTM) and quantum phase interference. The union of classical and quantum behavior in these nanomaterials makes SMMs ideal candidates for high-density information storage and quantum computing. However, environmental coupling factors (nuclear spins, phonons, neighboring molecules) must be minimized if such applications are ever to be fully realized. The focus of this work is making small structural changes in well-known manganese SMMs in order to drastically enhance the overall magnetic and quantum properties of the system. Well-isolated molecules of high crystalline quality should lead to well-defined energetic and spectral properties as well. An advantage of SMMs over bulk magnetic materials is that they can be chemically altered from a "bottom-up" approach providing a synthetic tool for tuning magnetic properties. This systematic approach is utilized in the work presented herein by incorporating bulky ligands and/or counterions to "isolate" the magnetic core of [Mn4] dicubane SMMs. Reducing intermolecular interactions in the crystal lattice (neighboring molecules, solvate molecules, dipolar interactions) is an important step toward developing viable quantum computing devices. Detailed bulk magnetic studies as well as single crystal magnetization hysteresis and high-frequency EPR studies on these sterically-isolated complexes show enhanced, and sometimes even unexpected, quantum dynamics. The importance of intra- and intermolecular interactions remains a common theme throughout this work, extending to other SMMs of various topology including

  12. Evaporation of liquid droplets of nano- and micro-meter size as a function of molecular mass and intermolecular interactions: experiments and molecular dynamics simulations.

    Hołyst, Robert; Litniewski, Marek; Jakubczyk, Daniel

    2017-09-13

    Transport of heat to the surface of a liquid is a limiting step in the evaporation of liquids into an inert gas. Molecular dynamics (MD) simulations of a two component Lennard-Jones (LJ) fluid revealed two modes of energy transport from a vapour to an interface of an evaporating droplet of liquid. Heat is transported according to the equation of temperature diffusion, far from the droplet of radius R. The heat flux, in this region, is proportional to temperature gradient and heat conductivity in the vapour. However at some distance from the interface, Aλ, (where λ is the mean free path in the gas), the temperature has a discontinuity and heat is transported ballistically i.e. by direct individual collisions of gas molecules with the interface. This ballistic transport reduces the heat flux (and consequently the mass flux) by the factor R/(R + Aλ) in comparison to the flux obtained from temperature diffusion. Thus it slows down the evaporation of droplets of sizes R ∼ Aλ and smaller (practically for sizes from 10 3 nm down to 1 nm). We analyzed parameter A as a function of interactions between molecules and their masses. The rescaled parameter, A(k B T b /ε 11 ) 1/2 , is a linear function of the ratio of the molecular mass of the liquid molecules to the molecular mass of the gas molecules, m 1 /m 2 (for a series of chemically similar compounds). Here ε 11 is the interaction parameter between molecules in the liquid (proportional to the enthalpy of evaporation) and T b is the temperature of the gas in the bulk. We tested the predictions of MD simulations in experiments performed on droplets of ethylene glycol, diethylene glycol, triethylene glycol and tetraethylene glycol. They were suspended in an electrodynamic trap and evaporated into dry nitrogen gas. A changes from ∼1 (for ethylene glycol) to approximately 10 (for tetraethylene glycol) and has the same dependence on molecular parameters as obtained for the LJ fluid in MD simulations. The value of x = A

  13. Desensitization and recovery of metastable intermolecular composites

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

    2010-09-07

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

  14. Mössbauer spectroscopic and powder X-ray diffraction studies on incorporation of gaseous organic molecules into intermolecular nano-voids of mixed-valence trinuclear iron pentafluorobenzoate complex

    Sakai, Yoichi; Onaka, Satoru; Ogiso, Ryo; Takayama, Tsutomu; Takahashi, Masashi; Nakamoto, Tadahiro

    2013-01-01

    Incorporation of gaseous organic molecules into polycrystalline mixed-valence trinuclear iron (Fe 3+ ,Fe 3+ ,Fe 2+ ) pentafluorobenzoate complex Fe 3 O(C 6 F 5 COO) 6 (C 5 H 5 N) 3 with intermolecular nano-voids was studied by 57 Fe-Mössbauer spectroscopic and powder XRD measurements. Organic-molecule incorporation was mainly chased by using iron-valence fluctuation observed in a Mössbauer spectrum, and also researched supportively by a powder XRD technique. (author)

  15. Ab initio study of the CO-N2 complex: a new highly accurate intermolecular potential energy surface and rovibrational spectrum

    Cybulski, Hubert; Henriksen, Christian; Dawes, Richard

    2018-01-01

    A new, highly accurate ab initio ground-state intermolecular potential-energy surface (IPES) for the CO-N2 complex is presented. Thousands of interaction energies calculated with the CCSD(T) method and Dunning's aug-cc-pVQZ basis set extended with midbond functions were fitted to an analytical...... function. The global minimum of the potential is characterized by an almost T-shaped structure and has an energy of -118.2 cm-1. The symmetry-adapted Lanczos algorithm was used to compute rovibrational energies (up to J = 20) on the new IPES. The RMSE with respect to experiment was found to be on the order...... of 0.038 cm-1 which confirms the very high accuracy of the potential. This level of agreement is among the best reported in the literature for weakly bound systems and considerably improves on those of previously published potentials....

  16. Spectroscopic study on the intermolecular interaction of SO{sub 2} absorption in poly-ethylene glycol+H{sub 2}O systems

    He, Zhiqiang; Liu, Jinrong; Zhang, Jianbin; Zhang, Na [Inner Mongolia University of Technology, Huhhot (China)

    2014-03-15

    Poly-Ethylene Glycol (PEG) 300+H{sub 2}O solutions (PEGWs) has been used as a promising medium for the absorption of SO{sub 2}. We investigated the UV, FTIR, {sup 1}H-NMR, and fluorescence spectra in the absorption processes of SO{sub 2} in PEGWs to present an important absorption mechanism. Based on the spectral results, the possibility of intermolecular hydrogen bond formation by hydroxyl oxygen atom in the PEG molecule with hydrogen atom in H{sub 2}O and S…O interaction formation by the oxygen atoms in PEG with the sulfur atom in SO{sub 2} are discussed. This shows that the spectral changes may be due to the formation of -CH{sub 2}CH{sub 2}O(H)…HOH… and -CH{sub 2}-CH{sub 2}-O(CH{sub 2}-CH{sub 2}-)…HOH… in PEGWs and the formation of -CH{sub 2}CH{sub 2}OH…OSO…, and intermolecular S…O interaction between PEG and SO{sub 2} as the formation of -CH{sub 2}CH{sub 2}OCH{sub 2}CH{sub 2}O(H)…(O)S(O)… and -CH{sub 2}-CH{sub 2}-O(CH{sub 2}-CH{sub 2}-) …(O)S(O)…. The existence of these bonds benefits the absorption and desorption processes of SO{sub 2} in PEGWs.

  17. Studies in Chemical Dynamics

    Rabitz, Herschel; Ho, Tak-San

    2003-01-01

    This final report draws together the research carried from February, 1986 through January, 2003 concerning a series of topics in chemical dynamics. The specific areas of study include molecular collisions, chemical kinetics, data inversion to extract potential energy surfaces, and model reduction of complex kinetic systems

  18. Programmable display of DNA-protein chimeras for controlling cell-hydrogel interactions via reversible intermolecular hybridization.

    Zhang, Zhaoyang; Li, Shihui; Chen, Niancao; Yang, Cheng; Wang, Yong

    2013-04-08

    Extensive studies have been recently carried out to achieve dynamic control of cell-material interactions primarily through physicochemical stimulation. The purpose of this study was to apply reversible intermolecular hybridization to program cell-hydrogel interactions in physiological conditions based on DNA-antibody chimeras and complementary oligonucleotides. The results showed that DNA oligonucleotides could be captured to and released from the immobilizing DNA-functionalized hydrogels with high specificity via DNA hybridization. Accordingly, DNA-antibody chimeras were captured to the hydrogels, successfully inducing specific cell attachment. The cell attachment to the hydrogels reached the plateau at approximately half an hour after the functionalized hydrogels and the cells were incubated together. The attached cells were rapidly released from the bound hydrogels when triggering complementary oligonucleotides were introduced to the system. However, the capability of the triggering complementary oligonucleotides in releasing cells was affected by the length of intermolecular hybridization. The length needed to be at least more than 20 base pairs in the current experimental setting. Notably, because the procedure of intermolecular hybridization did not involve any harsh condition, the released cells maintained the same viability as that of the cultured cells. The functionalized hydrogels also exhibited the potential to catch and release cells repeatedly. Therefore, this study demonstrates that it is promising to regulate cell-material interactions dynamically through the DNA-programmed display of DNA-protein chimeras.

  19. Mechanism of Intermolecular Electron Transfer in Bionanostructures

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

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

  20. Characterizing the Polymer:Fullerene Intermolecular Interactions

    Sweetnam, Sean; Vandewal, Koen; Cho, Eunkyung; Risko, Chad; Coropceanu, Veaceslav; Salleo, Alberto; Bredas, Jean-Luc; McGehee, Michael D.

    2016-01-01

    the polymer and fullerene, there is not a consensus on the nature of these interactions. In this work, we use a combination of Raman spectroscopy, charge transfer state absorption, and density functional theory calculations to show that the intermolecular

  1. Characterizing the Polymer:Fullerene Intermolecular Interactions

    Sweetnam, Sean

    2016-02-02

    Polymer:fullerene solar cells depend heavily on the electronic coupling of the polymer and fullerene molecular species from which they are composed. The intermolecular interaction between the polymer and fullerene tends to be strong in efficient photovoltaic systems, as evidenced by efficient charge transfer processes and by large changes in the energetics of the polymer and fullerene when they are molecularly mixed. Despite the clear presence of these strong intermolecular interactions between the polymer and fullerene, there is not a consensus on the nature of these interactions. In this work, we use a combination of Raman spectroscopy, charge transfer state absorption, and density functional theory calculations to show that the intermolecular interactions do not appear to be caused by ground state charge transfer between the polymer and fullerene. We conclude that these intermolecular interactions are primarily van der Waals in nature. © 2016 American Chemical Society.

  2. Intermolecular effects on the radiogenic formation of electron-capture phosphorus-centered radicals. A single-crystal ESR study of diastereoisomeric precursors

    Aagaard, O.M.; Janssen, R.A.J.; de Waal, B.F.M.; Buck, H.M. (Eindhoven Univ. of Technology (Netherlands))

    1990-01-31

    ESR experiments on X-irradiated single crystals of the 2R,4S,5R and 2S,4S,5R diastereoisomers of 2-chloro-3,4-dimethyl-5-phenyl-1,3,2-oxazaphospholidine 2-sulfide reveal that the yield of radiogenic electron-capture reactions in the solid state strongly depends on intermolecular interactions in the crystal. In the present case a high yield of P-Cl three-electron-bond phosphoranyl radical anions is found in crystals of the 2R,4S,5R isomer, whereas no radical formation can be detected for the 2S,4S,5R isomer. An analysis of nonbonded interactions with neighboring molecules reveals that the geometry relaxation necessary for the radical stabilization is easily accommodated in crystals of the 2R,4S,SR isomer but not in the 2S,4S,5R isomer, explaining the observed difference in electron-capture efficiency. Experiments on radical formation in a MeTHF host matrix give further insight into the importance of the environment on radiogenic radical formation. The possible concurrent effect of the matrix on the electronic configuration and spin density distribution of the resulting phosphoranyl radical is discussed.

  3. Intermolecular effects on the radiogenic formation of electron-capture phosphorus-centered radicals. A single-crystal ESR study of diastereoisomeric precursors

    Aagaard, O.M.; Janssen, R.A.J.; de Waal, B.F.M.; Buck, H.M.

    1990-01-01

    ESR experiments on X-irradiated single crystals of the 2R,4S,5R and 2S,4S,5R diastereoisomers of 2-chloro-3,4-dimethyl-5-phenyl-1,3,2-oxazaphospholidine 2-sulfide reveal that the yield of radiogenic electron-capture reactions in the solid state strongly depends on intermolecular interactions in the crystal. In the present case a high yield of P-Cl three-electron-bond phosphoranyl radical anions is found in crystals of the 2R,4S,5R isomer, whereas no radical formation can be detected for the 2S,4S,5R isomer. An analysis of nonbonded interactions with neighboring molecules reveals that the geometry relaxation necessary for the radical stabilization is easily accommodated in crystals of the 2R,4S,SR isomer but not in the 2S,4S,5R isomer, explaining the observed difference in electron-capture efficiency. Experiments on radical formation in a MeTHF host matrix give further insight into the importance of the environment on radiogenic radical formation. The possible concurrent effect of the matrix on the electronic configuration and spin density distribution of the resulting phosphoranyl radical is discussed

  4. Molecular simulation of fluids with non-identical intermolecular potentials: Thermodynamic properties of 10-5 + 12-6 Mie potential binary mixtures

    Stiegler, Thomas; Sadus, Richard J.

    2015-01-01

    General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form

  5. Theoretical study of intermolecular energy transfer involving electronically excited molecules: He(1S) + H2(B 1Σ/sub u/+)

    Grimes, R.M.

    1986-11-01

    To further understanding of gas phase collision dynamics involving electronically-excited molecules, a fully quantum mechanical study of He + H 2 (B 1 Σ/sub u/ + ) was undertaken. Iterative natural orbital configuration interaction (CI) calculations were performed to obtain the interaction potential between He and H 2 (B 1 Σ/sub u/ + ). The potential energy surface (PES) is highly anisotropic and has a van der Waals well of about 0.03 eV for C/sub 2v/ approach. Avoided PES crossings occur with He + H 2 (E,F 1 Σ/sub g/ + ) and with He + H 2 (X 1 Σ/sub g/ + ) and cause a local maximum and a deep minimum in the He + H 2 (B 1 Σ/sub u/ + ) PES, respectively. The crossing with He + H 2 (X 1 Σ/sub g/ + ) provides a mechanism for fluorescence quenching. The computed CI energies were combined with previous multi-reference double excitation CI calculations and fit with analytic functions for convenience in scattering calculations. Accurate dipole polarizabilities and quadrupole moment of H 2 (B 1 Σ/sub u/ + ) were computed for use in the multipole expansion, which is the analytic form of the long-range PES. 129 refs., 28 figs., 35 tabs

  6. Effects of pair correlation functions on intermolecular nuclear relaxation by translational and rotational diffusion in liquids

    Fries, P.

    1978-01-01

    In order to study the intermolecular relaxation due to magnetic dipolar interactions, we calculate the spectral densities resulting from random translational and rotational motions of spherical molecules carrying off-centre spins. The relative translational motion is treated in the frame-work of a general diffusion equation (the Smoluchowski equation) which takes into account the existence of effective forces between the molecules. This model implies a pair correlation function. i.e. a non unifom relative distribution of the molecules. The analytical calculations are carried out by taking correctly into account the hard sphere boundary conditions for the molecules. Explicit numerical calculations of the spectral densities are performed using finite difference methods and the pair correlation function of Verlet and Weiss obtained by computer experiments. The resulting calculations allow one to interpret the relaxation exhibited by benzene and some of its monohalogen derivatives which has been measured by Jonas et al. at various pressures. The effects of pair correlation and eccentricity contribute to a noticeable enhancement of the spectral densities, especially as the frequency increases. The translational correlation times calculated from the Stokes formula and those deduced from intermolecular relaxation studies are compared. It is shown that in order to distinguish which of the dynamical models is appropriate, measurements must be made as a function of frequency [fr

  7. Cohesion: a scientific history of intermolecular forces

    Rowlinson, J. S

    2002-01-01

    .... The final section gives an account of the successful use in the 20th century of quantum mechanics and statistical mechanics to resolve most of the remaining problems. Throughout the last 300 years there have been periods of tremendous growth in our understanding of intermolecular forces but such interest proved to be unsustainable, and long periods of...

  8. Intermolecular cleavage by UmuD-like mutagenesis proteins

    McDonald, John P.; Frank, Ekaterina G.; Levine, Arthur S.; Woodgate, Roger

    1998-01-01

    The activity of a number of proteins is regulated by self-processing reactions. Elegant examples are the cleavage of the prokaryotic LexA and λCI transcriptional repressors and the UmuD-like mutagenesis proteins. Various studies support the hypothesis that LexA and λCI cleavage reactions are predominantly intramolecular in nature. The recently described crystal structure of the Escherichia coli UmuD′ protein (the posttranslational cleavage product of the UmuD protein) suggests, however, that the region of the protein corresponding to the cleavage site is at least 50 Å away from the catalytic active site. We considered the possibility, therefore, that the UmuD-like proteins might undergo self-processing that, in contrast to LexA and λCI, occurs via an intermolecular rather than intramolecular reaction. To test this hypothesis, we introduced into E. coli compatible plasmids with mutations at either the cleavage or the catalytic site of three UmuD-like proteins. Cleavage of these proteins only occurs in the presence of both plasmids, indicating that the reaction is indeed intermolecular in nature. Furthermore, this intermolecular reaction is completely dependent upon the multifunctional RecA protein and leads to the restoration of cellular mutagenesis in nonmutable E. coli strains. Intermolecular cleavage of a biotinylated UmuD active site mutant was also observed in vitro in the presence of the wild-type UmuD′ protein, indicating that in addition to the intact UmuD protein, the normal cleavage product (UmuD′) can also act as a classical enzyme. PMID:9465040

  9. Efficiency of the intermolecular interaction of salicylic acid neutral form and monoanion with Cd2 + ion studied by methods of absorption and fluorescence

    Lavrik, N. L.; Mulloev, N. U.

    2018-02-01

    The methods of absorption and fluorescence were used to study the efficiency of the interaction between salicylic acid derivatives SAD (neutral SA form and SA monoanion) and Cd2 + ions (in CdBr2 salt) within the range pH = 1.5 ÷ 8. The efficiency was determined from the change in both the absorption band contour and the fluorescence intensity of various SAD forms. It has been established that depending on the SAD form, the addition of CdBr2 to a starting solution leads to the formation of additional absorption for both the shorter wave lengths in the absorption spectrum of the neutral form (at pH 4). In the fluorescence spectra, the intensity was observed to increase for the neutral SAD form (at pH 4) after addition of CdBr2. The spectral changes were interpreted in the framework of common notions about the effect of three physicochemical factors that determine the interaction between the SAD and the Cd2 + ion and affect the parameters of absorption and fluorescence spectra. These factors are: (1) the decrease in pH after addition of CdBr2 to the SAD solution, (2) the decrease in the efficiency of the H-bonding of SAD molecules to the water ones, and (3) the existence of electrostatic ion-ion interaction between the HSal- monoanion and the Cd2 + ion. The bimolecular fluorescence quenching constants Kq of HSal- monoanion fluorescence quenching by the Cd2 + ion appeared to be substantially less than those of the quenching which would follow either the dynamic (diffusion) or the concentration (static) mechanisms.

  10. Studying Dynamics in Business Networks

    Andersen, Poul Houman; Anderson, Helen; Havila, Virpi

    1998-01-01

    This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland......This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland...

  11. Digital communication through intermolecular fluorescence modulation.

    Raymo, F M; Giordani, S

    2001-06-14

    [see reaction]. Ultraminiaturized processors incorporating molecular components can be developed only after devising efficient strategies to communicate signals at the molecular level. We have demonstrated that a three-state molecular switch responds to ultraviolet light, visible light, and H+, attenuating the emission intensity of a fluorescent probe. Intermolecular communication is responsible for the transduction of three input signals into a single optical output. The behavior of the communicating ensemble of molecules corresponds to that of a logic circuit incorporating seven gates.

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

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

    2012-02-01

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

  13. Modeling Adsorption-Desorption Processes at the Intermolecular Interactions Level

    Varfolomeeva, Vera V.; Terentev, Alexey V.

    2018-01-01

    Modeling of the surface adsorption and desorption processes, as well as the diffusion, are of considerable interest for the physical phenomenon under study in ground tests conditions. When imitating physical processes and phenomena, it is important to choose the correct parameters to describe the adsorption of gases and the formation of films on the structural materials surface. In the present research the adsorption-desorption processes on the gas-solid interface are modeled with allowance for diffusion. Approaches are proposed to describe the adsorbate distribution on the solid body surface at the intermolecular interactions level. The potentials of the intermolecular interaction of water-water, water-methane and methane-methane were used to adequately modeling the real physical and chemical processes. The energies calculated by the B3LYP/aug-cc-pVDZ method. Computational algorithms for determining the average molecule area in a dense monolayer, are considered here. Differences in modeling approaches are also given: that of the proposed in this work and the previously approved probabilistic cellular automaton (PCA) method. It has been shown that the main difference is due to certain limitations of the PCA method. The importance of accounting the intermolecular interactions via hydrogen bonding has been indicated. Further development of the adsorption-desorption processes modeling will allow to find the conditions for of surface processes regulation by means of quantity adsorbed molecules control. The proposed approach to representing the molecular system significantly shortens the calculation time in comparison with the use of atom-atom potentials. In the future, this will allow to modeling the multilayer adsorption at a reasonable computational cost.

  14. Syntheses of planar 1,5,2,4,6,8-dithiotetrazocine derivatives and thermodynamic study on intermolecular charge transfer for developing efficient organic solar cell

    Zhang, Chao-Zhi, E-mail: zhangchaozhi@nuist.edu.cn [Department of Chemistry, Nanjing University of Information Science & Technology, Nanjing 210044 (China); Shen, Dan [Department of Chemistry, Nanjing University of Information Science & Technology, Nanjing 210044 (China); Yuan, Yang [Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Nanjing University of Information Science & Technology, Nanjing 210044 (China); Song, Ming-Xia; Li, Shi-Juan [Department of Chemistry, Nanjing University of Information Science & Technology, Nanjing 210044 (China); Cao, Hui, E-mail: yccaoh@hotmail.com [Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Nanjing University of Information Science & Technology, Nanjing 210044 (China)

    2016-07-01

    A series of planar 1,5,2,4,6,8-dithiotetrazocine derivatives were synthesized for study on charge transfer at donor/acceptor interface. The fluorescence quenching spectra, and the highest occupied molecular orbital (−6.10 ∼ −6.25 eV) and the lowest unoccupied molecular orbital (−3.45 ∼ −3.58 eV) energy levels of these 1,5,2,4,6,8-dithiotetrazocine derivatives show that they would be potential acceptor materials. Based on theoretical calculations, thermodynamic study on charge transfer at donor/acceptor interface was carried out. The results of experiments and theoretical calculations show that the electrons could transfer spontaneously from poly(3-hexylthiophene) to these acceptors. The percentages of fluorescence quenching increase with negative Gibbs free energy values increasing in the charge transfer procedures. Therefore, short circuit current values of organic solar cells would increase with the Gibbs free energy values increasing. This paper suggests a useful way for developing efficient organic solar cells. - Highlights: • Syntheses of planar 1,5,2,4,6,8-dithiotetrazocine derivatives for develop effective acceptor. • Electrons at excited state in P3HT could transfer spontaneously to these acceptors. • Thermodynamic study on charge transfer at donor/acceptor interface. • Short circuit currents would be predicted by Gibbs free energy in procedure of charge transfer.

  15. Intermolecular interactions in the condensed phase

    Christensen, Anders S.; Kromann, Jimmy Charnley; Jensen, Jan Halborg

    2017-01-01

    To facilitate further development of approximate quantum mechanical methods for condensed phase applications, we present a new benchmark dataset of intermolecular interaction energies in the solution phase for a set of 15 dimers, each containing one charged monomer. The reference interaction energy...... and solution phases. As most approximate QM methods are parametrized and evaluated using data measured or calculated in the gas phase, the dataset represents an important first step toward calibrating QM based methods for application in the condensed phase where polarization and exchange repulsion need...

  16. Studies in chemical dynamics

    Kuppermann, A.

    1978-01-01

    Progress made in the following studies is reported: low-energy electron scattering; variable-angle photoelectron spectroscopy; laser photochemistry and spectroscopy; and collisions in crossed molecular beams

  17. New bases for the evaluation of interaction energies: An ab initio study of the CO-Ne van der Waals complex intermolecular potential and ro-vibrational spectrum

    Bouzon Capelo, Silvia; Baranowska-Laczkowska, Angelika; Fernandez, Berta

    2011-01-01

    Graphical abstract: CO-Ne IPES. Highlights: → From the LPol, MLPol, and aug-pc-2 bases we obtained new bases for the evaluation of CO-Ne interaction energies. → We checked the bases on the evaluation of the rovibrational spectrum. → The results were satisfactory, being the new bases more efficient than those previously available. - Abstract: Recently we have derived new efficient basis sets for the evaluation of interaction energies in the X-Y (X, Y = He, Ne, Ar) van der Waals complexes. Here we extend the study to the CO-Ne complex. For this, we start with a systematic basis set study, where the LPol, MLPol and Jensen's aug-pc-2 basis sets are considered as starting point (for the Ne atom LPol bases are developed). As reference we take interaction energy results obtained with Dunning's augmented correlation consistent polarized valence basis sets. In all cases we test extensions with different sets of midbond functions. With the selected bases we evaluate CCSD(T) interaction potentials, and to check the potentials further, we obtain the ro-vibrational spectrum of the complex. The results are compared to the available experimental data.

  18. Solvent effect on the intermolecular proton transfer of the Watson and Crick guanine-cytosine and adenine-thymine base pairs: a polarizable continuum model study.

    Romero, Eduardo E; Hernandez, Florencio E

    2018-01-03

    Herein we present our results on the study of the double proton transfer (DPT) mechanism in the adenine-thymine (AT) and guanine-cytosine (GC) base pairs, both in gas phase and in solution. The latter was modeled using the polarizable continuum method (PCM) in different solvents. According to our DFT calculations, the DPT may occur for both complexes in a stepwise mechanism in condensate phase. In gas phase only the GC base pair exhibits a concerted DPT mechanism. Using the Wigner's tunneling corrections to the transition state theory we demonstrate that such corrections are important for the prediction of the rate constants of both systems in gas and in condensate phase. We also show that (i) as the polarity of the medium decreases the equilibrium constant of the DPT reaction increases in both complexes, and (ii) that the equilibrium constant in the GC complex is four orders of magnitude larger than in AT. This observation suggests that the spontaneous mutations in DNA base pairs are more probable in GC than in AT.

  19. Intermolecular-directed reactivity in solid media. Radiogenic formation of phosphorus-centered radicals in chiral diphosphine disulfides studied by ESR

    Aagaard, O.M.; Janssen, R.A.J.; de Waal, B.F.M.; Buck, H.M. (Eindhoven Univ. of Technology (Netherlands)); Kanters, J.A.; Schouten, A. (State Univ. of Utrecht (Netherlands))

    1990-07-04

    Single-crystal, powder, and frozen-matrix ESR experiments have been performed to study the radiogenic electron-capture properties of several diastereoisomeric and asymmetric diphosphine disulfides (R{sub 1}R{sub 2}P(S)P(S)R{sub 3}R{sub 4}). The principal values of the hyperfine couplings of several phosphorus-centered radical configurations are determined and related to the spin density distribution. Attention is focused on the strong differences in radiogenic properties, observed between the meso and racemic forms of phenyl- and tolyl-substituted diphosphine disulfides. The most striking result is that X irradiation of the crystalline meso compounds MePhP(S)P(S)MePh, Me(p-Tol)P(S)P(S)Me(p-Tol), and Ph(PhCH{sub 2})P(S)P(S)Ph(CH{sub 2}Ph) does not lead to the formation of a three-electron bond P-P {sigma}* radical but invariably results in configurations in which the unpaired electron is primarily localized on one half of the molecule. X irradiation of the corresponding racemic forms, on the other hand, gives rise to P-P {sigma}* configurations.

  20. Model-free nuclear magnetic resonance study of intermolecular free energy landscapes in liquids with paramagnetic Ln3+ spotlights: theory and application to Arg-Gly-Asp.

    Fries, Pascal H

    2012-01-28

    We propose an easily applicable method for investigating the pair distribution function of a lanthanide Ln(3+) complex LnL (L = ligand) with respect to any solvent or solute molecule A carrying observable nuclear spins. Let r be the distance of Ln(3+) to the observed nuclear spin I. We derive a simple expression of the experimental value of the configurational average of 1/r(6) in terms of longitudinal paramagnetic relaxation (rate) enhancements (PREs) of the spin I measured on a standard high-resolution NMR spectrometer and due to well-chosen concentrations of LnL complexes in which Ln(3+) is a fast-relaxing paramagnetic lanthanide or the slowly-relaxing gadolinium Gd(3+). The derivation is justified in the general case of a molecule A which is by turns in a bound state where it follows the complex and a free state where it moves independently. It rests on the expression of the underlying PRE theory in terms of the angle-dependent pair distribution function of LnL and A. The simplifications of this theory in the high-field regime and under the condition of fast exchange between bound and free states are carefully discussed. We also show that original information on the angle dependence of the molecular pair distribution function can be gained from the measured paramagnetic dipolar shifts induced by complexed fast-relaxing Ln(3+) ions. The method is illustrated by the case study of the anionic Lnttha(3-) = [Ln(3+)(ttha)](3-) (ttha(6-) = triethylene tetraamine hexacetate) complex interacting with the biologically important tripeptide Arg-Gly-Asp (RGD) which carries peripheral ionic groups. The usefulness of an auxiliary reference outer sphere probe solute is emphasized. © 2012 American Institute of Physics

  1. Study of estuarine dynamics

    Genders, S.

    1979-01-01

    A case study of a shallow, well mixed fjord illustrates the use of radioactive and an activable tracer. An instantaneous injection of the rare earth lanthanum was used as an activable tracer to determine residence-time and internal recirculation in the fjord system. An instantaneous injection of bromine-82 was used to investigate tae bypass of water from a harbour area through a power plant cooling water system to a partly enclosed basin of the fjord. Instantaneous releases of bromine-82 were further used for short time studies of the primary spread and transport of river water discharged to the inner section of the fjord system. (Author) [pt

  2. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    Venkatesha R. Hathwar

    2015-09-01

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

  3. The iodine molecule insights into intra- and intermolecular perturbation in diatomic molecules

    Lukashov, Sergey; Pravilov, Anatoly

    2018-01-01

    This book presents experimental and theoretical spectroscopic studies performed over the last 25 years on the iodine molecule’s excited states and their perturbations. It is going to be of interest to researchers who study intra- and intermolecular perturbations in diatomic molecules and more complex systems. The book offers a detailed treatment of the nonadiabatic perturbations of valence, ion pair and Rydberg states induced by intramolecular as well as intermolecular interactions in collisions or in weakly-bound complexes. It also provides an overview of current instrumentation and techniques as well as theoretical approaches describing intra- and intermolecular perturbations. The authors are experts in the use of spectroscopy for the study of intrinsic and collision-induced perturbations in diatomic iodine. They introduced new methods of two- and three-step optical population of the iodine ion-pair states. The iodine molecule has 23 valence states correlating with three dissociation limits, 20 so-called ...

  4. Theoretical studies of combustion dynamics

    Bowman, J.M. [Emory Univ., Atlanta, GA (United States)

    1993-12-01

    The basic objectives of this research program are to develop and apply theoretical techniques to fundamental dynamical processes of importance in gas-phase combustion. There are two major areas currently supported by this grant. One is reactive scattering of diatom-diatom systems, and the other is the dynamics of complex formation and decay based on L{sup 2} methods. In all of these studies, the authors focus on systems that are of interest experimentally, and for which potential energy surfaces based, at least in part, on ab initio calculations are available.

  5. Effect of intermolecular dipole-dipole interactions on interfacial supramolecular structures of C3-symmetric hexa-peri-hexabenzocoronene derivatives.

    Mu, Zhongcheng; Shao, Qi; Ye, Jun; Zeng, Zebing; Zhao, Yang; Hng, Huey Hoon; Boey, Freddy Yin Chiang; Wu, Jishan; Chen, Xiaodong

    2011-02-15

    Two-dimensional (2D) supramolecular assemblies of a series of novel C(3)-symmetric hexa-peri-hexabenzocoronene (HBC) derivatives bearing different substituents adsorbed on highly oriented pyrolytic graphite were studied by using scanning tunneling microscopy at a solid-liquid interface. It was found that the intermolecular dipole-dipole interactions play a critical role in controlling the interfacial supramolecular assembly of these C(3)-symmetric HBC derivatives at the solid-liquid interface. The HBC molecule bearing three -CF(3) groups could form 2D honeycomb structures because of antiparallel dipole-dipole interactions, whereas HBC molecules bearing three -CN or -NO(2) groups could form hexagonal superstructures because of a special trimeric arrangement induced by dipole-dipole interactions and weak hydrogen bonding interactions ([C-H···NC-] or [C-H···O(2)N-]). Molecular mechanics and dynamics simulations were performed to reveal the physics behind the 2D structures as well as detailed functional group interactions. This work provides an example of how intermolecular dipole-dipole interactions could enable fine control over the self-assembly of disklike π-conjugated molecules.

  6. Structural modeling and intermolecular correlation of liquid chlorine dioxide

    Ogata, Norio; Hironori, Shimakura; Kawakita, Yukinobu; Ohara, Yukoji; Kohara, Shinji; Takeda, Shinichi

    2009-01-01

    Chlorine dioxide (ClO 2 ) is water-soluble yellow gas at room temperature. It has long been used as a disinfectant of tap water and various commodities owing to its strong oxidizing activity against various microbial proteins. The oxidizing activity is believed to be due to the presence of unpaired electron in its molecular orbital. Despite wealth of physicochemical studies of gaseous ClO 2 , little is known about liquid ClO 2 , especially about fine molecular structure and intermolecular interactions of liquid ClO 2 . The purpose of this study is to elucidate the fine structure and intermolecular orientations of ClO 2 molecules in its liquid state using a high-energy X-ray diffraction technique. The measurements of liquid ClO 2 were carried out at -50 to 0 degree Celsius using a two-axis diffractometer installed at the BL04B2 beamline in the third-generation synchrotron radiation facility SPring-8 (Hyogo, Japan). The incident X-ray beamline was 113.4 keV in energy and 0.1093 Armstrong in wavelength from a Si(111) monochromator with the third harmonic reflection. Liquid ClO 2 held in a quartz capillary tube was placed in a temperature-controlled vacuum chamber. We obtained a structure factor S(Q) to a range of Q = 0.3-30 Amstrong -1 and a pair distribution function g(r) upon Fourier transform of the S(Q). The total g(r) showed peaks at 1.46, 2.08, 2.48, 3.16 and 4.24 Armstrong. From intramolecular bond lengths of 1.46 Armstrong for Cl-O and 2.48 Armstrong for O-O, O-Cl-O bond angle was estimated to be 116.1 degrees. Peaks at 3.16 and 4.24 Armstrong in the total g(r) strongly indicate presence of specific intermolecular orientations of ClO 2 molecules that are distinct from those observed as a dimer in the solid phase ClO 2 . This view was further supported by molecular simulation using a reverse Monte Carlo method (RMC). (author)

  7. Direct measurements of intermolecular forces by chemical force microscopy

    Vezenov, Dmitri Vitalievich

    1999-12-01

    Detailed description of intermolecular forces is key to understanding a wide range of phenomena from molecular recognition to materials failure. The unique features of atomic force microscopy (AFM) to make point contact force measurements with ultra high sensitivity and to generate spatial maps of surface topography and forces have been extended to include measurements between well-defined organic molecular groups. Chemical modification of AFM probes with self-assembled monolayers (SAMs) was used to make them sensitive to specific molecular interactions. This novel chemical force microscopy (CFM) technique was used to probe forces between different molecular groups in a range of environments (vacuum, organic liquids and aqueous solutions); measure surface energetics on a nanometer scale; determine pK values of the surface acid and base groups; measure forces to stretch and unbind a short synthetic DNA duplex and map the spatial distribution of specific functional groups and their ionization state. Studies of adhesion forces demonstrated the important contribution of hydrogen bonding to interactions between simple organic functionalities. The chemical identity of the tip and substrate surfaces as well as the medium had a dramatic effect on adhesion between model monolayers. A direct correlation between surface free energy and adhesion forces was established. The adhesion between epoxy polymer and model mixed SAMs varied with the amount of hydrogen bonding component in the monolayers. A consistent interpretation of CFM measurements in polar solvents was provided by contact mechanics models and intermolecular force components theory. Forces between tips and surfaces functionalized with SAMs terminating in acid or base groups depended on their ionization state. A novel method of force titration was introduced for highly local characterization of the pK's of surface functional groups. The pH-dependent changes in friction forces were exploited to map spatially the

  8. Effects of Intermolecular Coupling on Excimer Formation and Singlet Fission

    Mauck, Catherine McKay

    The development of organic photovoltaic devices benefits from understanding the fundamental processes underlying charge generation in thin films of organic semiconductors. This dissertation exploits model systems of pi-stacked chromophores such as perylene-3,4:9,10-bis(dicarboximide) (PDI) and 3,6-bis(aryl)diketopyrrolopyrrole (DPP) to study these processes using ultrafast electronic and vibrational spectroscopy. In particular, the characterization of covalent molecular dimers, thin films, and solution aggregates can reveal how supramolecular order affects photophysical properties. PDI and DPP are organic semiconductors that have been widely studied in organic photovoltaics, due to their strong visible absorption and excellent chemical stability. As solution-phase monomers, they are highly fluorescent, but in the thin film environment of photovoltaic devices these planar aromatic molecules couple to one another, stacking largely through pi-pi interactions. In self-assembled stacks of PDI, strong interchromophore coupling may disrupt charge separation through the formation of excimer states, preventing the generation of free carriers. By studying molecular dimers of PDI with different pi-stacked geometry, femtosecond visible pump mid-infrared probe spectroscopy allows direct observation of the structural dynamics associated with excimer state relaxation, showing that this low-energy state is primarily coupled to the core modes that shift as planarization and rotation lead to the most stable excimer geometry. PDI is also able to undergo singlet fission in thin films and aggregates. Singlet fission is the process in which a singlet excited state is downconverted into two triplet excitons, when the energy of its first singlet excited state is at least twice the energy of the lowest triplet state in an appropriately coupled molecular system. This spin-allowed, ultrafast process enables a theoretical yield of two charge carriers per incident photon, making it a

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

    Xantheas, Sotiris S.

    2004-05-01

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

  10. Studies of ground-state dynamics in isolated species by ionization-detected stimulated Raman techniques

    Felker, P.M. [Univ. of California, Los Angeles (United States)

    1993-12-01

    First, the author aims to develop methods of nonlinear Raman spectroscopy for application in studies of sparse samples. Second, the author wishes to apply such methods to structural and dynamical studies of species (molecules, complexes, and clusters) in supersonic molecular beams. In the past year, the author has made progress in several areas. The first pertains to the application of mass-selective ionization-detected stimulated Raman spectroscopies (IDSRS) to the size-specific vibrational spectroscopy of solute-solvent{sub n} clusters. The second involves the application of IDSRS methods to studies of jet-cooled benzene clusters. The third pertains to the use of IDSRS methods in the study of intermolecular vibrational transitions in van der Waals complexes.

  11. Similarities between intra- and intermolecular hydrogen bonds in RNA kissing complexes found by means of cross-correlated relaxation

    Dittmer, Jens; Kim, Chul-Hyun; Bodenhausen, Geoffrey

    2003-01-01

    The bond lengths and dynamics of intra- and intermolecular hydrogen bonds in an RNA kissing complex have been characterized by determining the NMR relaxation rates of various double- and triple-quantum coherences that involve an imino proton and two neighboring nitrogen-15 nuclei belonging to opposite bases. New experiments allow one to determine the chemical shift anisotropy of the imino protons. The bond lengths derived from dipolar relaxation and the lack of modulations of the nitrogen chemical shifts indicate that the intermolecular hydrogen bonds which hold the kissing complex together are very similar to the intramolecular hydrogen bonds in the double-stranded stem of the RNA

  12. Molecular dynamics study of silver

    Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.

    1995-03-01

    We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs

  13. Measuring Intermolecular Binding Energies by Laser Spectroscopy.

    Knochenmuss, Richard; Maity, Surajit; Féraud, Géraldine; Leutwyler, Samuel

    2017-02-22

    The ground-state dissociation energy, D0(S0), of isolated intermolecular complexes in the gas phase is a fundamental measure of the interaction strength between the molecules. We have developed a three-laser, triply resonant pump-dump-probe technique to measure dissociation energies of jet-cooled M•S complexes, where M is an aromatic chromophore and S is a closed-shell 'solvent' molecule. Stimulated emission pumping (SEP) via the S0→S1 electronic transition is used to precisely 'warm' the complex by populating high vibrational levels v" of the S0 state. If the deposited energy E(v") is less than D0(S0), the complex remains intact, and is then mass- and isomer-selectively detected by resonant two-photon ionization (R2PI) with a third (probe) laser. If the pumped level is above D0(S0), the hot complex dissociates and the probe signal disappears. Combining the fluorescence or SEP spectrum of the cold complex with the SEP breakoff of the hot complex brackets D0(S0). The UV chromophores 1-naphthol and carbazole were employed; these bind either dispersively via the aromatic rings, or form a hydrogen bond via the -OH or -NH group. Dissociation energies have been measured for dispersively bound complexes with noble gases (Ne, Kr, Ar, Xe), diatomics (N2, CO), alkanes (methane to n-butane), cycloalkanes (cyclopropane to cycloheptane), and unsaturated compounds (ethene, benzene). Hydrogen-bond dissociation energies have been measured for H2O, D2O, methanol, ethanol, ethers (oxirane, oxetane), NH3 and ND3.

  14. All rights reserved Intermolecular Model Potentials and Virial ...

    ADOWIE PERE

    Intermolecular Model Potentials and Virial Coefficients from Acoustic Data. 1* ... method of cluster expansion. Its merit is that, ... their determination is by the analyses of isothermal p- ρ-y data ... Carlo simulation method to calculate volumetric.

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

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

    2013-11-28

    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.

  16. Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: Does a stronger acid make a stiffer hydrogen bond?

    Houjou, Hirohiko

    2011-10-01

    Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m-1 for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

  17. He-, Ne-, and Ar-phosgene intermolecular potential energy surfaces

    Munteanu, Cristian R.; Henriksen, Christian; Felker, Peter M.

    2013-01-01

    Using the CCSD(T) model, we evaluated the intermolecular potential energy surfaces of the He-, Ne-, and Ar-phosgene complexes. We considered a representative number of intermolecular geometries for which we calculated the corresponding interaction energies with the augmented (He complex) and doub...... of the complexes, providing valuable results for future experimental investigations. Comparing our results to those previously available for other phosgene complexes, we suggest that the results for Cl2-phosgene should be revised....

  18. Dynamical studies of molecular systems. Progress report, February 1, 1980-October 27, 1980

    Rabitz, H.

    1980-01-01

    Research was carried out in the general areas of collision dynamics and chemical kinetics. Research on the following topics was pursued: computational kinetics and sensitivity analysis of hydrogen-oxygen combustion; chemical kinetic functional sensitivity analysis, elementary sensitivities; the selective preparation of excited vibrational states using the stimulated resonance raman effect; an exactly soluble many channel scattering model; further developments and applications of sensitivity analysis to collisional energy transfer; sensitivity analysis of rotational energy transfer processes to the intermolecular potential; a review of vibrational rotational collision processes; sensitivity analysis of differential cross sections to the intermolecular potential; and a non-local formulation of inelastic scattering as a basis for practical approximations

  19. On the influence of the intermolecular potential on the wetting properties of water on silica surfaces

    Pafong, E.; Geske, J.; Drossel, B.

    2016-09-01

    We study the wetting properties of water on silica surfaces using molecular dynamics (MD) simulations. To describe the intermolecular interaction between water and silica atoms, two types of interaction potential models are used: the standard BródkA and Zerda (BZ) model and the Gulmen and Thompson (GT) model. We perform an in-depth analysis of the influence of the choice of the potential on the arrangement of the water molecules in partially filled pores and on top of silica slabs. We find that at moderate pore filling ratios, the GT silica surface is completely wetted by water molecules, which agrees well with experimental findings, while the commonly used BZ surface is less hydrophilic and is only partially wetted. We interpret our simulation results using an analytical calculation of the phase diagram of water in partially filled pores. Moreover, an evaluation of the contact angle of the water droplet on top of the silica slab reveals that the interaction becomes more hydrophilic with increasing slab thickness and saturates around 2.5-3 nm, in agreement with the experimentally found value. Our analysis also shows that the hydroaffinity of the surface is mainly determined by the electrostatic interaction, but the van der Waals interaction nevertheless is strong enough that it can turn a hydrophobic surface into a hydrophilic surface.

  20. Ground state analytical ab initio intermolecular potential for the Cl2-water system

    Hormain, Laureline; Monnerville, Maurice; Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón

    2015-01-01

    The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl 2 molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl 2 − H 2 O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl 2 interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl 2 on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results

  1. Studying the Impact of Modified Saccharides on the Molecular Dynamics and Crystallization Tendencies of Model API Nifedipine.

    Kaminska, E; Tarnacka, M; Wlodarczyk, P; Jurkiewicz, K; Kolodziejczyk, K; Dulski, M; Haznar-Garbacz, D; Hawelek, L; Kaminski, K; Wlodarczyk, A; Paluch, M

    2015-08-03

    Molecular dynamics of pure nifedipine and its solid dispersions with modified carbohydrates as well as the crystallization kinetics of active pharmaceutical ingredient (API) above and below the glass transition temperature were studied in detail by means of broadband dielectric spectroscopy (BDS), differential scanning calorimetry (DSC), and X-ray diffraction method. It was found that the activation barrier of crystallization increases in molecular dispersions composed of acetylated disaccharides, whereas it slightly decreases in those consisting of modified monocarbohydrates for the experiments carried out above the glass transition temperature. As shown by molecular dynamics simulations it can be related to the strength, character, and structure of intermolecular interactions between API and saccharides, which vary dependently on the excipient. Long-term physical stability studies showed that, in solid dispersions consisting of acetylated maltose and acetylated sucrose, the crystallization of nifedipine is dramatically slowed down, although it is still observable for a low concentration of excipients. With increasing content of modified carbohydrates, the crystallization of API becomes completely suppressed. This is most likely due to additional barriers relating to the intermolecular interactions and diffusion of nifedipine that must be overcome to trigger the crystallization process.

  2. Quantifying intermolecular interactions of ionic liquids using cohesive energy densities

    2017-01-01

    For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced, is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, cedIP, where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, cedC+A, where the ionic vapour constituents are isolated ions. A cedIP dataset is presented for 64 ILs. For the first time an experimental cedC+A, a measure of the strength of the total intermolecular interaction for an IL, is presented. cedC+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between cedIP and the inverse of the molecular volume. A good linear correlation is found between IL cedIP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to cedIP. These findings show that cedIP is very important for understanding IL intermolecular interactions, in spite of cedIP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined. PMID:29308254

  3. Quantifying intermolecular interactions of ionic liquids using cohesive energy densities.

    Lovelock, Kevin R J

    2017-12-01

    For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced , is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, ced IP , where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, ced C+A , where the ionic vapour constituents are isolated ions. A ced IP dataset is presented for 64 ILs. For the first time an experimental ced C+A , a measure of the strength of the total intermolecular interaction for an IL, is presented. ced C+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between ced IP and the inverse of the molecular volume. A good linear correlation is found between IL ced IP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to ced IP . These findings show that ced IP is very important for understanding IL intermolecular interactions, in spite of ced IP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined.

  4. Studies in Chaotic adiabatic dynamics

    Jarzynski, C.

    1994-01-01

    Chaotic adiabatic dynamics refers to the study of systems exhibiting chaotic evolution under slowly time-dependent equations of motion. In this dissertation the author restricts his attention to Hamiltonian chaotic adiabatic systems. The results presented are organized around a central theme, namely, that the energies of such systems evolve diffusively. He begins with a general analysis, in which he motivates and derives a Fokker-Planck equation governing this process of energy diffusion. He applies this equation to study the open-quotes goodnessclose quotes of an adiabatic invariant associated with chaotic motion. This formalism is then applied to two specific examples. The first is that of a gas of noninteracting point particles inside a hard container that deforms slowly with time. Both the two- and three-dimensional cases are considered. The results are discussed in the context of the Wall Formula for one-body dissipation in nuclear physics, and it is shown that such a gas approaches, asymptotically with time, an exponential velocity distribution. The second example involves the Fermi mechanism for the acceleration of cosmic rays. Explicit evolution equations are obtained for the distribution of cosmic ray energies within this model, and the steady-state energy distribution that arises when this equation is modified to account for the injection and removal of cosmic rays is discussed. Finally, the author re-examines the multiple-time-scale approach as applied to the study of phase space evolution under a chaotic adiabatic Hamiltonian. This leads to a more rigorous derivation of the above-mentioned Fokker-Planck equation, and also to a new term which has relevance to the problem of chaotic adiabatic reaction forces (the forces acting on slow, heavy degrees of freedom due to their coupling to light, fast chaotic degrees)

  5. Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.

    Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Tsai, Chung-Jun; Nussinov, Ruth

    2007-11-01

    We investigate Abeta(17-42) protofibril structures in solution using molecular dynamics simulations. Recently, NMR and computations modeled the Abeta protofibril as a longitudinal stack of U-shaped molecules, creating an in-parallel beta-sheet and loop spine. Here we study the molecular architecture of the fibril formed by spine-spine association. We model in-register intermolecular beta-sheet-beta-sheet associations and study the consequences of Alzheimer's mutations (E22G, E22Q, E22K, and M35A) on the organization. We assess the structural stability and association force of Abeta oligomers with different sheet-sheet interfaces. Double-layered oligomers associating through the C-terminal-C-terminal interface are energetically more favorable than those with the N-terminal-N-terminal interface, although both interfaces exhibit high structural stability. The C-terminal-C-terminal interface is essentially stabilized by hydrophobic and van der Waals (shape complementarity via M35-M35 contacts) intermolecular interactions, whereas the N-terminal-N-terminal interface is stabilized by hydrophobic and electrostatic interactions. Hence, shape complementarity, or the "steric zipper" motif plays an important role in amyloid formation. On the other hand, the intramolecular Abeta beta-strand-loop-beta-strand U-shaped motif creates a hydrophobic cavity with a diameter of 6-7 A, allowing water molecules and ions to conduct through. The hydrated hydrophobic cavities may allow optimization of the sheet association and constitute a typical feature of fibrils, in addition to the tight sheet-sheet association. Thus, we propose that Abeta fiber architecture consists of alternating layers of tight packing and hydrated cavities running along the fibrillar axis, which might be possibly detected by high-resolution imaging.

  6. Intermolecular Interactions in Ternary Glycerol–Sample–H2O

    Westh, Peter; Rasmussen, Erik Lumby; Koga, Yoshikata

    2011-01-01

    We studied the intermolecular interactions in ternary glycerol (Gly)–sample (S)–H2O systems at 25 °C. By measuring the excess partial molar enthalpy of Gly, HGlyEHEGly, we evaluated the Gly–Gly enthalpic interaction, HGly-GlyEHEGly--Gly, in the presence of various samples (S). For S, tert...... little effect on HGly-GlyEHEGly--Gly. This contrasts with our earlier studies on 1P–S–H2O in that Na+, F− and Cl− are found as hydration centers from the induced changes on HIP-IPEHEIP--IP in the presence of S, while Br−, I−, and SCN− are found to act as hydrophiles. In comparison with the Hofmeister...... ranking of these ions, the kosmotropes are hydration centers and the more kosmotropic the higher the hydration number, consistent with the original Hofmeister’s concept of “H2O withdrawing power.” Br−, I− and SCN−, on the other hand, acted as hydrophiles and the more chaotropic they are the more...

  7. The origins of the directionality of noncovalent intermolecular interactions.

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

    2016-01-05

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

  8. Dynamical study of liquid aluminium

    Dubey, G.S.; Chaturvedi, D.K.

    1979-09-01

    Recent molecular dynamics data of Ebbsjoe et al. in liquid aluminium have been analysed through the memory function formalism. Two forms of the memory functions which have correct asymptotic limit at large wavenumbers but accounts for interatomic correlations in a different manner are considered. The results for ω 2 s(q, ω) obtained from both models are compared with experimental data. (author)

  9. INTERACTIONS: DESIGN, IMPLEMENTATION AND EVALUATION OF A COMPUTATIONAL TOOL FOR TEACHING INTERMOLECULAR FORCES IN HIGHER EDUCATION

    Francisco Geraldo Barbosa

    2015-12-01

    Full Text Available Intermolecular forces are a useful concept that can explain the attraction between particulate matter as well as numerous phenomena in our lives such as viscosity, solubility, drug interactions, and dyeing of fibers. However, studies show that students have difficulty understanding this important concept, which has led us to develop a free educational software in English and Portuguese. The software can be used interactively by teachers and students, thus facilitating better understanding. Professors and students, both graduate and undergraduate, were questioned about the software quality and its intuitiveness of use, facility of navigation, and pedagogical application using a Likert scale. The results led to the conclusion that the developed computer application can be characterized as an auxiliary tool to assist teachers in their lectures and students in their learning process of intermolecular forces.

  10. A quantum mechanical study of water adsorption on the (110) surfaces of rutile SnO₂ and TiO₂: investigating the effects of intermolecular interactions using hybrid-exchange density functional theory.

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

    2014-10-21

    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).

  11. Connecting Protein Structure to Intermolecular Interactions: A Computer Modeling Laboratory

    Abualia, Mohammed; Schroeder, Lianne; Garcia, Megan; Daubenmire, Patrick L.; Wink, Donald J.; Clark, Ginevra A.

    2016-01-01

    An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several…

  12. Phase transitions in liquids with directed intermolecular bonding

    Son, L.; Ryltcev, R.

    2005-01-01

    Liquids with quasi - chemical bonding between molecules are described in terms of vertex model. It is shown that this bonding results in liquid - liquid phase transition, which occurs between phases with different mean density of intermolecular bonds. The transition may be suggested to be a universal phenomena for those liquids.

  13. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    Mundell, Donald W.

    2007-01-01

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

  14. Boiling points of halogenated ethanes: an explanatory model implicating weak intermolecular hydrogen-halogen bonding.

    Beauchamp, Guy

    2008-10-23

    This study explores via structural clues the influence of weak intermolecular hydrogen-halogen bonds on the boiling point of halogenated ethanes. The plot of boiling points of 86 halogenated ethanes versus the molar refraction (linked to polarizability) reveals a series of straight lines, each corresponding to one of nine possible arrangements of hydrogen and halogen atoms on the two-carbon skeleton. A multiple linear regression model of the boiling points could be designed based on molar refraction and subgroup structure as independent variables (R(2) = 0.995, standard error of boiling point 4.2 degrees C). The model is discussed in view of the fact that molar refraction can account for approximately 83.0% of the observed variation in boiling point, while 16.5% could be ascribed to weak C-X...H-C intermolecular interactions. The difference in the observed boiling point of molecules having similar molar refraction values but differing in hydrogen-halogen intermolecular bonds can reach as much as 90 degrees C.

  15. Enhanced intermolecular forces in supramolecular polymer nanocomposites

    F. Lin

    2017-09-01

    Full Text Available Ureido-pyrimidone (Upy can dimerize in a self-complementary array of quadruple hydrogen bonds. In this paper, supramolecular polymer composites were prepared by blending Upy functionalized nanosilica with Upy end-capped polycarbonatediol. Surface characteristics of Upy functionalized nanosilica and influences of supramolecular forces on interfacial binding were researched. Fourier transform infrared spectroscopy (FTIR, Nuclear magnetic resonance (NMR and Gel permeation chromatography (GPC were used to characterize the synthesized molecules. Grafting ratio of Upy segments on the surface of nanosilica was analysed by Thermogravimetic analysis (TGA. Hydrophobicity and morphology of Upy modified nanosilica were analysed by Contact angle tester and Scanning electron microscope (SEM. Furthermore, dynamic thermo mechanical properties, mechanical properties and distribution of nanosilica in supramolecular polymer composites were also researched. Compared with the matrix resin, tensile stress and young's modulus of supramolecular polymer composites containing 5 wt% modified nanosilica were increased by 292 and 198% respectively.

  16. Theoretical studies of combustion dynamics

    Bowman, J.M.

    1986-01-01

    The reactions of O( 3 P)+H 2 , D 2 , and HD are the focus of this research. Their approximate three-dimensional quantum calculations of the rate constant for both the ground and first excited vibrational states of the above reactions were completed last year. Comparisons of the calculated rate constants, isotope effects and branching ratios have been made with available experimental work and also with the variational transition state theory calculations. The main conclusion of that paper is that tunneling plays a major role in the reaction dynamics at room temperature and below

  17. A comparative study of ibuprofen and ketoprofen glass-forming liquids by molecular dynamics simulations

    Ottou Abe, M. T.; Correia, N. T.; Ndjaka, J. M. B.; Affouard, F.

    2015-10-01

    In this paper, structural and dynamical properties of ibuprofen and ketoprofen glass-forming liquids have been investigated by means of molecular dynamics simulations. Molecular mobility of both materials is analyzed with respect to the different inter-molecular linear/cyclic hydrogen bonding associations. For ibuprofen, the dominant organization is found to be composed of small hydrogen bonding aggregates corresponding to cyclic dimers through the carboxyl group. For ketoprofen, the propensity of cyclic dimers is significantly reduced by the formation of hydrogen bonds with the ketone oxygen of the molecule altering the hydrogen bond (HB) associating structures that can be formed and thus molecular dynamics. The issue of the presence/absence of the peculiar low frequency Debye-type process in dielectric relaxation spectroscopy (DRS) data in these materials is addressed. Results obtained from simulations confirm that the Debye process originates from the internal cis-trans conversion of the —COOH carboxyl group. It is shown that the specific intermolecular HB structures associated to a given profen control the main dynamical features of this conversion, in particular its separation from the α-process, which make it detectable or not from DRS. For ibuprofen, the possible role of the —CCCO torsion motion, more "local" than the —COOH motion since it is less influenced by the intermolecular HBs, is suggested in the microscopic origin of the quite intense secondary γ-relaxation process detected from DRS.

  18. Decay correction methods in dynamic PET studies

    Chen, K.; Reiman, E.; Lawson, M.

    1995-01-01

    In order to reconstruct positron emission tomography (PET) images in quantitative dynamic studies, the data must be corrected for radioactive decay. One of the two commonly used methods ignores physiological processes including blood flow that occur at the same time as radioactive decay; the other makes incorrect use of time-accumulated PET counts. In simulated dynamic PET studies using 11 C-acetate and 18 F-fluorodeoxyglucose (FDG), these methods are shown to result in biased estimates of the time-activity curve (TAC) and model parameters. New methods described in this article provide significantly improved parameter estimates in dynamic PET studies

  19. Theoretical study of intermolecular energy transfer involving electronically excited molecules: He(/sup 1/S) + H/sub 2/(B /sup 1/. sigma. /sub u//sup +/). [Solution for coupled channel equations

    Grimes, R.M.

    1986-11-01

    To further understanding of gas phase collision dynamics involving electronically-excited molecules, a fully quantum mechanical study of He + H/sub 2/(B /sup 1/..sigma../sub u//sup +/) was undertaken. Iterative natural orbital configuration interaction (CI) calculations were performed to obtain the interaction potential between He and H/sub 2/(B /sup 1/..sigma../sub u//sup +/). The potential energy surface (PES) is highly anisotropic and has a van der Waals well of about 0.03 eV for C/sub 2v/ approach. Avoided PES crossings occur with He + H/sub 2/(E,F /sup 1/..sigma../sub g//sup +/) and with He + H/sub 2/(X /sup 1/..sigma../sub g//sup +/) and cause a local maximum and a deep minimum in the He + H/sub 2/(B /sup 1/..sigma../sub u//sup +/) PES, respectively. The crossing with He + H/sub 2/(X /sup 1/..sigma../sub g//sup +/) provides a mechanism for fluorescence quenching. The computed CI energies were combined with previous multi-reference double excitation CI calculations and fit with analytic functions for convenience in scattering calculations. Accurate dipole polarizabilities and quadrupole moment of H/sub 2/(B /sup 1/..sigma../sub u//sup +/) were computed for use in the multipole expansion, which is the analytic form of the long-range PES. 129 refs., 28 figs., 35 tabs.

  20. Intermolecular Force Field Parameters Optimization for Computer Simulations of CH4 in ZIF-8

    Phannika Kanthima

    2016-01-01

    Full Text Available The differential evolution (DE algorithm is applied for obtaining the optimized intermolecular interaction parameters between CH4 and 2-methylimidazolate ([C4N2H5]− using quantum binding energies of CH4-[C4N2H5]− complexes. The initial parameters and their upper/lower bounds are obtained from the general AMBER force field. The DE optimized and the AMBER parameters are then used in the molecular dynamics (MD simulations of CH4 molecules in the frameworks of ZIF-8. The results show that the DE parameters are better for representing the quantum interaction energies than the AMBER parameters. The dynamical and structural behaviors obtained from MD simulations with both sets of parameters are also of notable differences.

  1. Highly Stereoselective Intermolecular Haloetherification and Haloesterification of Allyl Amides

    Soltanzadeh, Bardia; Jaganathan, Arvind; Staples, Richard J.

    2016-01-01

    An organocatalytic and highly regio-, diastereo-, and enantioselective intermolecular haloetherification and haloesterification reaction of allyl amides is reported. A variety of alkene substituents and substitution patterns are compatible with this chemistry. Notably, electronically unbiased alkene substrates exhibit exquisite regio- and diastereoselectivity for the title transformation. We also demonstrate that the same catalytic system can be used in both chlorination and bromination reactions of allyl amides with a variety of nucleophiles with little or no modification. PMID:26110812

  2. Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips

    Mönig, Harry; Amirjalayer, Saeed; Timmer, Alexander; Hu, Zhixin; Liu, Lacheng; Díaz Arado, Oscar; Cnudde, Marvin; Strassert, Cristian Alejandro; Ji, Wei; Rohlfing, Michael; Fuchs, Harald

    2018-05-01

    Atomic force microscopy is an impressive tool with which to directly resolve the bonding structure of organic compounds1-5. The methodology usually involves chemical passivation of the probe-tip termination by attaching single molecules or atoms such as CO or Xe (refs 1,6-9). However, these probe particles are only weakly connected to the metallic apex, which results in considerable dynamic deflection. This probe particle deflection leads to pronounced image distortions, systematic overestimation of bond lengths, and in some cases even spurious bond-like contrast features, thus inhibiting reliable data interpretation8-12. Recently, an alternative approach to tip passivation has been used in which slightly indenting a tip into oxidized copper substrates and subsequent contrast analysis allows for the verification of an oxygen-terminated Cu tip13-15. Here we show that, due to the covalently bound configuration of the terminal oxygen atom, this copper oxide tip (CuOx tip) has a high structural stability, allowing not only a quantitative determination of individual bond lengths and access to bond order effects, but also reliable intermolecular bond characterization. In particular, by removing the previous limitations of flexible probe particles, we are able to provide conclusive experimental evidence for an unusual intermolecular N-Au-N three-centre bond. Furthermore, we demonstrate that CuOx tips allow the characterization of the strength and configuration of individual hydrogen bonds within a molecular assembly.

  3. Spatial inhomogeneity in spectra and exciton dynamics in porphyrin ...

    inhomogeneity. This is elucidated by time-resolved confocal microscopy. ... dynamics of such supramolecular aggregates. Weisman ... protein scaffold and faithfully represents a biomimetic reminiscent .... increased intermolecular interactions.

  4. Structures in dynamics finite dimensional deterministic studies

    Broer, HW; van Strien, SJ; Takens, F

    1991-01-01

    The study of non-linear dynamical systems nowadays is an intricate mixture of analysis, geometry, algebra and measure theory and this book takes all aspects into account. Presenting the contents of its authors' graduate courses in non-linear dynamical systems, this volume aims at researchers who wish to be acquainted with the more theoretical and fundamental subjects in non-linear dynamics and is designed to link the popular literature with research papers and monographs. All of the subjects covered in this book are extensively dealt with and presented in a pedagogic

  5. Proton tunnelling in intermolecular hydrogen bonds

    Horsewill, A J [Nottingham Univ. (United Kingdom); Johnson, M R [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France); Trommsdorff, H P [Grenoble-1 Univ., 38 (France)

    1997-04-01

    The wavefunctions of particles extend beyond the classically accessible regions of potential energy-surfaces (PES). A manifestation of this partial delocalization is the quantum-mechanical tunneling effect which enables a particle to escape from a metastable potential-well. Tunnelling is most important for the lightest atoms, so that the determination of its contribution to proton transfer, one of the most fundamental chemical reactions, is an important issue. QENS and NMR techniques have been employed to study the motion of protons in the hydrogen bond of benzoic-acid crystals, a system which has emerged as a particularly suitable model since proton transfer occurs in a near symmetric double-well potential. The influence of quantum tunnelling was revealed and investigated in these experiments. This work provides an experimental benchmark for theoretical descriptions of translational proton-tunnelling. (author). 7 refs.

  6. Vibrational properties of the amide group in acetanilide: A molecular-dynamics study

    Campa, Alessandro; Giansanti, Andrea; Tenenbaum, Alexander

    1987-09-01

    A simplified classical model of acetanilide crystal is built in order to study the mechanisms of vibrational energy transduction in a hydrogen-bonded solid. The intermolecular hydrogen bond is modeled by an electrostatic interaction between neighboring excess charges on hydrogen and oxygen atoms. The intramolecular interaction in the peptide group is provided by a dipole-charge interaction. Forces are calculated up to second-order terms in the atomic displacements from equilibrium positions; the model is thus a chain of nonlinear coupled oscillators. Numerical molecular-dynamics experiments are performed on chain segments of five molecules. The dynamics is ordered, at all temperatures. Energy is widely exchanged between the stretching and the bending of the N-H bond, with characteristic times of the order of 0.2 ps. Energy transduction through the H bond is somewhat slower and of smaller amplitude, and is strongly reduced when the energies of the two bound molecules are very different: This could reduce the dissipation of localized energy fluctuations.

  7. Effects of sodium salt types on the intermolecular interaction of sodium alginate/antarctic krill protein composite fibers.

    Zhang, Rui; Guo, Jing; Liu, Yuanfa; Chen, Shuang; Zhang, Sen; Yu, Yue

    2018-06-01

    Sodium alginate (SA) and antarctic krill protein (AKP) were blended to fabricate the SA/AKP composite fibers by the conventional wet spinning method using 5% CaCl 2 as coagulation solution. The sodium salt was added to the SA/AKP solution to adjust the ionization degree and intermolecular interaction of composite system. The main purpose of this study is to investigate the influences of sodium salt types (NaCl, CH 3 COONa, Na 2 SO 4 ) on the intermolecular interaction of SA/AKP composite fibers. The intermolecular interaction, morphology, crystallinity, thermal stability and mechanical properties of SA/AKP composite fibers were analyzed by fourier transform infrared spectroscopy (FT-IR), scanning electron microscope (SEM), x-ray diffraction (XRD), thermogravimetric analysis (TGA). The results show that the types of sodium salt have obvious influences on the content of both β-sheet, intermolecular hydrogen bond, breaking strength and surface morphology in SA/AKP composite fibers, but have a negligible effect on the crystallinity and thermal stability. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Multimegawatt dynamic NEP PMAD study

    Metcalf, K.J.

    1993-01-01

    The National Aeronautics and Space Administration Lewis Research Center (NASA LeRC) is developing a Fortran--based model of a complete nuclear electric propulsion (NEP) vehicle to be used for piloted or cargo missions to the Moon or Mars. The proposed vehicle will use either a Brayton or K-Rankine power conversion cycle, and either ion or magnetoplasmadynamic (MPD) thrusters. In support of this effort, Rocketdyne evaluated various power management and distribution (PMAD) approaches and selected a low-frequency design that is based on the direct use of the alternator voltage and frequency for power transmission. This approach was compared with dc and high-frequency ac designs, and selected on the basis of mass, efficiency, and qualitative assessments of power quality, reliability and development costs. This low-frequency architecture will be used as the reference in future NEP PMAD studies and for the subsequent Fortran model development

  9. Intermolecular proton transfer in anionic complexes of uracil with alcohols

    Haranczyk, Maciej; Rak, Janusz; Gutowski, Maciej S.; Radisic, Dunja; Stokes, Sarah T.; Bowen, Kit H.

    2005-01-01

    A series of eighteen alcohols (ROH) has been designed with an enthalpy of deprotonation (H DP ) in a range of 13.8-16.3 eV. The effects of excess electron attachment to the binary alcohol-uracil (ROH...U) complexes have been studied at the density functional level with a B3LYP exchange-correlation functional and at the second order Moeller-Plesset perturbation theory level. The photoelectron spectra of anionic complexes of uracil with three alcohols (ethanol, 2,2,3,3,3-pentafluoroethanol and 1,1,1,3,3,3-hexafluoro-2-propanol) have been measured with 2.54 eV photons. For ROHs with deprotonation enthalpies larger than 14.8 eV only the ROH...U - minimum exists on the potential energy surface of the anionic complex. For alcohols with deprotonation enthalpies in a range of 14.3-14.8 eV two minima might exist on the anionic potential energy surface, which correspond to the RO - ...HU . and ROH...U - structures. For ROHs with deprotonation enthalpies smaller than 14.3 eV, the excess electron attachment to the ROH...U complex always induces a barrier-free proton transfer from the hydroxyl group of ROH to the O8 atom of U, with the product being RO - ...HU . . A driving force for the intermolecular proton transfer is to stabilize the excess negative charge localized on a orbital of uracil. Therefore, these complexes with proton transferred to the anionic uracil are characterized by larger values of electron vertical detachment energy (VDE). The values of VDE for anionic complexes span a range from 1.0 to 2.3 eV and roughly correlate with the acidity of alcohols. However, there is a gap of ∼0.5 eV in the values of VDE, which separates the two families, ROH...U - and RO - ...HU . , of anionic complexes. The energy of stabilization for the anionic complexes spans a range from 0.6 to 1.7 eV and roughly correlates with the acidity of alcohols. The measured photoelectron spectra are in good agreement with the theoretical predictions

  10. Formation of an intermolecular charge-transfer compound in UHV codeposited tetramethoxypyrene and tetracyanoquinodimethane

    Medjanik, K.; Perkert, S.; Naghavi, S.

    2010-01-01

    Ultrahigh vacuum (UHV)-deposited films of the mixed phase of tetramethoxypyrene and tetracyanoquinodimethane (TMP -TCNQ ) on gold have been studied using ultraviolet photoelectron spectroscopy (UPS), x-ray diffraction (XRD), infrared (IR) spectroscopy, and scanning tunneling spectroscopy (STS......). The formation of an intermolecular charge-transfer (CT) compound is evident from the appearance of new reflexes in XRD (d =0.894nm and d =0.677nm). A softening of the CN stretching vibration (redshift by 7 cm⊃-1) of TCNQ is visible in the IR spectra, being indicative of a CT on the order of 0.3e from TMP...

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

    Macduff O. Okuom

    2013-01-01

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

  12. Molecular dynamics studies of superionic conductors

    Rahman, A.; Vashishta, P.

    1983-01-01

    Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

  13. Computer processing of dynamic scintigraphic studies

    Ullmann, V.

    1985-01-01

    The methods are discussed of the computer processing of dynamic scintigraphic studies which were developed, studied or implemented by the authors within research task no. 30-02-03 in nuclear medicine within the five year plan 1981 to 85. This was mainly the method of computer processing radionuclide angiography, phase radioventriculography, regional lung ventilation, dynamic sequential scintigraphy of kidneys and radionuclide uroflowmetry. The problems are discussed of the automatic definition of fields of interest, the methodology of absolute volumes of the heart chamber in radionuclide cardiology, the design and uses are described of the multipurpose dynamic phantom of heart activity for radionuclide angiocardiography and ventriculography developed within the said research task. All methods are documented with many figures showing typical clinical (normal and pathological) and phantom measurements. (V.U.)

  14. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    Mori, Yukie, E-mail: mori.yukie@ocha.ac.jp; Masuda, Yuichi

    2015-09-08

    Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl{sub 4}, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the {sup 17

  15. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    Mori, Yukie; Masuda, Yuichi

    2015-01-01

    Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl 4 , acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17 O and 1

  16. Intermolecular interactions between σ- and π-holes of bromopentafluorobenzene and pyridine: computational and experimental investigations.

    Yang, Fang-Ling; Yang, Xing; Wu, Rui-Zhi; Yan, Chao-Xian; Yang, Fan; Ye, Weichun; Zhang, Liang-Wei; Zhou, Pan-Pan

    2018-04-25

    The characters of σ- and π-holes of bromopentafluorobenzene (C6F5Br) enable it to interact with an electron-rich atom or group like pyridine which possesses an electron lone-pair N atom and a π ring. Theoretical studies of intermolecular interactions between C6F5Br and C5H5N have been carried out at the M06-2X/aug-cc-pVDZ level without and with the counterpoise method, together with single point calculations at M06-2X/TZVP, wB97-XD/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels. The σ- and π-holes of C6F5Br exhibiting positive electrostatic potentials make these sites favorably interact with the N atom and the π ring of C5H5N with negative electrostatic potentials, leading to five different dimers connected by a σ-holen bond, a σ-holeπ bond or a π-holeπ bond. Their geometrical structures, characteristics, nature and spectroscopy behaviors were systematically investigated. EDA analyses reveal that the driving forces in these dimers are different. NCI, QTAIM and NBO analyses confirm the existence of intermolecular interactions formed via σ- and π-holes of C6F5Br and the N atom and the π ring of C5H5N. The experimental IR and Raman spectra gave us important information about the formation of molecular complexes between C6F5Br and C5H5N. We expect that the results could provide valuable insights into the investigation of intermolecular interactions involving σ- and π-holes.

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

    Hobbs, M.L.

    1997-12-01

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

  18. An approach to the intermolecular energy in pure liquids

    GAbriel Hernández de la Torre

    2010-07-01

    Full Text Available Se propone un método para: estimar la energía potencial de repulsión de cualquier molécula central como una función de las densidades ortobáricas en líquidos puros no auto asociados; estimar los parámetros necesarios para calcular la energía de dispersión de London; calcular los números de coordinación promedio, distancias intermoleculares de interacción, diámetros moleculares y de grupos; en moléculas globulares, moléculas planas y parafinas normales.

  19. Contributions to the Study of Dynamic Absorbers, a Case Study

    Monica Balcau

    2012-01-01

    Full Text Available Dynamic absorbers are used to reduce torsional vibrations. This paper studies the effect of a dynamic absorber attached to a mechanical system formed of three reduced masses which are acted on by one, two or three order x harmonics of a disruptive force.

  20. A study of the HEB longitudinal dynamics

    Larson, D.J.

    1993-12-01

    A study of the High Energy Booster (HEB) longitudinal dynamics is presented. Full derivations of ramp dependent longitudinal variables are given. The formulas assume that the input magnetic field and beam longitudinal emittance are known as a function of time, and that either the rf voltage or the rf bucket area are known as a function of time. Once these three inputs are specified, the formulas can be used to calculate values for all other longitudinal dynamics variables. The formulas have been incorporated into a single computer code named ELVIRA: Evaluation of Longitudinal Variables in Relativistic Accelerators. The ELVIRA code is documented here in detail. The ELVIRA code is used under two initial longitudinal emittance assumptions to plot ramp functions for the longitudinal dynamics design of the HEB as of May 5, 1992

  1. Study on dynamic performance of SOFC

    Zhan, Haiyang; Liang, Qianchao; Wen, Qiang; Zhu, Runkai

    2017-05-01

    In order to solve the problem of real-time matching of load and fuel cell power, it is urgent to study the dynamic response process of SOFC in the case of load mutation. The mathematical model of SOFC is constructed, and its performance is simulated. The model consider the influence factors such as polarization effect, ohmic loss. It also takes the diffusion effect, thermal effect, energy exchange, mass conservation, momentum conservation. One dimensional dynamic mathematical model of SOFC is constructed by using distributed lumped parameter method. The simulation results show that the I-V characteristic curves are in good agreement with the experimental data, and the accuracy of the model is verified. The voltage response curve, power response curve and the efficiency curve are obtained by this way. It lays a solid foundation for the research of dynamic performance and optimal control in power generation system of high power fuel cell stack.

  2. Hydrogen bonding analysis of hydroxyl groups in glucose aqueous solutions by a molecular dynamics simulation study

    Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Weng, Lin Dong; Zhang, Ning

    2012-01-01

    Molecular dynamics simulations have been performed to investigate hydrogen bonding characteristics of hydroxyl groups in glucose aqueous solutions with different concentrations. The hydrogen bonding abilities and strength of different O and H atom types have been calculated and compared. The acceptor/donor efficiencies have been predicted and it has been found that: (1) O2-HO2 and O3-HO3 are more efficient intramolecular hydrogen bonding acceptors than donors; (2) O1-HO1, O4-HO4 and O6-HO6 are more efficient intramolecular hydrogen bonding donors than acceptors; (5) O1-HO1 and O6-HO6 are more efficient intermolecular hydrogen bonding acceptors than donors while hydroxyl groups O2-HO2 and O4-HO4 are more efficient intermolecular hydrogen bonding donors than acceptors. The hydrogen bonding abilities of hydroxyl groups revealed that: (1) the hydrogen bonding ability of OH2-H w is larger than that of hydroxyl groups in glucose; (2) among the hydroxyl groups in glucose, the hydrogen bonding ability of O6-HO6 is the largest and the hydrogen bonding ability of O4-HO4 is the smallest; (3) the intermolecular hydrogen bonding ability of O6-HO6 is the largest; (4) the order for intramolecular hydrogen bonding abilities (from large to small) is O2-HO2, O1-HO1, O3-HO3, O6-HO6 and O4-HO4

  3. Applicability of mode-coupling theory to polyisobutylene: a molecular dynamics simulation study.

    Khairy, Y; Alvarez, F; Arbe, A; Colmenero, J

    2013-10-01

    The applicability of Mode Coupling Theory (MCT) to the glass-forming polymer polyisobutylene (PIB) has been explored by using fully atomistic molecular dynamics simulations. MCT predictions for the so-called asymptotic regime have been successfully tested on the dynamic structure factor and the self-correlation function of PIB main-chain carbons calculated from the simulated cell. The factorization theorem and the time-temperature superposition principle are satisfied. A consistent fitting procedure of the simulation data to the MCT asymptotic power-laws predicted for the α-relaxation regime has delivered the dynamic exponents of the theory-in particular, the exponent parameter λ-the critical non-ergodicity parameters, and the critical temperature T(c). The obtained values of λ and T(c) agree, within the uncertainties involved in both studies, with those deduced from depolarized light scattering experiments [A. Kisliuk et al., J. Polym. Sci. Part B: Polym. Phys. 38, 2785 (2000)]. Both, λ and T(c)/T(g) values found for PIB are unusually large with respect to those commonly obtained in low molecular weight systems. Moreover, the high T(c)/T(g) value is compatible with a certain correlation of this parameter with the fragility in Angell's classification. Conversely, the value of λ is close to that reported for real polymers, simulated "realistic" polymers and simple polymer models with intramolecular barriers. In the framework of the MCT, such finding should be the signature of two different mechanisms for the glass-transition in real polymers: intermolecular packing and intramolecular barriers combined with chain connectivity.

  4. A Molecular Dynamics Study of Lunasin | Singh | South African ...

    A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

  5. Molecular Dynamics Studies of Nanofluidic Devices

    Zambrano Rodriguez, Harvey Alexander

    of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

  6. Binding Cellulose and Chitosan via Intermolecular Inclusion Interaction: Synthesis and Characterisation of Gel

    Jiufang Duan

    2015-01-01

    Full Text Available A novel cellulose-chitosan gel was successfully prepared in three steps: (1 ferrocene- (Fc- cellulose with degrees of substitution (DS of 0.5 wt% was synthesised by ferrocenecarboxylic acid and cellulose within dimethylacetamide/lithium chloride (DMAc/LiCl; (2 the β-cyclodextrin (β-CD groups were introduced onto the chitosan chains by reacting chitosan with epichlorohydrin in dimethyl sulphoxide and a DS of 0.35 wt%; (3 thus, the cellulose-chitosan gel was obtained via an intermolecular inclusion interaction of Fc-cellulose and β-CD-chitosan in DMA/LiCl, that is, by an intermolecular inclusion interaction, between the Fc groups of cellulose and the β-CD groups on the chitosan backbone at room temperature. The successful synthesis of Fc-cellulose and β-CD-chitosan was characterised by 13C-NMR spectroscopy. The gel based on β-CD-chitosan and Fc-cellulose was formed under mild conditions which can engender autonomous healing between cut surfaces after 24 hours: the gel cannot self-heal while the cut surfaces were coated with a solution of a competitive guest (adamantane acid. The cellulose-chitosan complex made by this method underwent self-healing. Therefore, this study provided a novel method of expanding the application of chitosan by binding it with another polymer.

  7. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    Chavda, Bhavin R., E-mail: chavdabhavin9@gmail.com; Dubey, Rahul P.; Patel, Urmila H. [Department of Physics, Sardar Patel University, Vallabh Vidyanagar-388120, Gujarat (India); Gandhi, Sahaj A. [Bhavan’s Shri I.L. Pandya Arts-Science and Smt. J.M. shah Commerce College, Dakar, Anand -388001, Gujarat, Indian (India); Barot, Vijay M. [P. G. Center in Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat 383 215 (India)

    2016-05-06

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb –London –Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

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

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

    2010-01-01

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

  9. Dynamic MRI study for breast tumors

    Seki, Tsuneaki

    1990-01-01

    Application of MRI for diagnosis of breast tumors was retrospectively examined in 103 consecutive cases. Contrast enhancement, mostly by dynamic study, was performed in 83 cases using Gd-DTPA and 0.5 T superconductive apparatus. Results were compared to those of mammography and sonography. On dynamic study, carcinoma showed abrupt rise of signal intensity with clear-cut peak formation in early phase, while benign fibroadenoma showed slow rise of signal intensity and prolonged enhancement without peak formation. In 12 of 33 carcinomas (33%), peripheral ring enhancement was noted reflecting vascular stroma of histologic sections. All fibroadenomas showed homogenous enhancement without peripheral ring. In MRI, sensitivity, specificity, and accuracy were 86%, 96%, 91%. In mammography 82%, 95%, 87% and in ultrasonography 91%, 95%, 93%. Although MRI should not be regarded as routine diagnostic procedure because of expense and limited availability, it may afford useful additional information when standard mammographic findings are not conclusive. (author)

  10. Experimental studies of nonlinear beam dynamics

    Caussyn, D.D.; Ball, M.; Brabson, B.; Collins, J.; Curtis, S.A.; Derenchuck, V.; DuPlantis, D.; East, G.; Ellison, M.; Ellison, T.; Friesel, D.; Hamilton, B.; Jones, W.P.; Lamble, W.; Lee, S.Y.; Li, D.; Minty, M.G.; Sloan, T.; Xu, G.; Chao, A.W.; Ng, K.Y.; Tepikian, S.

    1992-01-01

    The nonlinear beam dynamics of transverse betatron oscillations were studied experimentally at the Indiana University Cyclotron Facility cooler ring. Motion in one dimension was measured for betatron tunes near the third, fourth, fifth, and seventh integer resonances. This motion is described by coupling between the transverse modes of motion and nonlinear field errors. The Hamiltonian for nonlinear particle motion near the third- and fourth-integer-resonance conditions has been deduced

  11. Nonlinear longitudinal dynamics studies at the ALS

    Byrd, J.M.; Cheng, W.-H.; De Santis, S.; Li, D.; Stupakov, G.; Zimmermann, F.

    1999-01-01

    We present a summary of results for a variety of studies of nonlinear longitudinal dynamics in the Advanced Light Source, an electron storage ring. These include observation of decoherence at injection, decay of an injected beam, forced synchrotron oscillations and diffusion from one bunch to the next. All of the measurements were made using a dual-scan streak camera which allowed the real-time observation of the longitudinal distribution of the electron beam

  12. Theoretical studies of chemical reaction dynamics

    Schatz, G.C. [Argonne National Laboratory, IL (United States)

    1993-12-01

    This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.

  13. Symmetry in the polarization expansion for intermolecular forces

    Chipman, D.M.; Hirschfelder, J.O.

    1980-01-01

    In the usual polarization expansion for intermolecular forces, exchange effects that determine the separations of energy levels within the manifold of interacting states are ignored. Previous low order calculations on simple physical systems have indicated that these exchange terms can be described reasonably well by an appropriate ad hoc symmetrization of the polarization wave function (the SYM-P method). But theoretical considerations suggest that the SYM-P method should be good for only one of the interacting states and not for the others in the manifold. Here this long standing apparent conflict between theoretical expectations and actual results is explained by consideration of a simple model system in which the relevant equations can be solved exactly. It is concluded that while the SYM-P method is potentially exact for only one of the interacting states, it may provide good approximations to the other states of the manifold in the case of large separations of the interacting subsystems

  14. Testing intermolecular potential functions using transport property data

    Clifford, A.A.; Dickinson, E.; Gray, P.; Scott, A.C.

    1975-01-01

    The viscosity of hydrogen has been measured at eight temperatures from 273 to 1060K, using a capillary-flow viscometer. The results have been used to test the repulsive part of a recently formulated H 2 /H 2 intermolecular potential function, obtained from molecular-beam measurements. Agreement between the experimental and predicted values for viscosity is within 3.5%, which corresponds approximately to the combined quoted uncertainties in the two sets of data. However, if the value of the distance parameter of the potential is reduced by about 1.5%, the agreement obtained is within 0.75% over the whole temperature range. This modified potential function gives better agreement with the available higher temperature viscosities and second virial coefficients. (author)

  15. Solar dynamic power system definition study

    Wallin, Wayne E.; Friefeld, Jerry M.

    1988-01-01

    The solar dynamic power system design and analysis study compared Brayton, alkali-metal Rankine, and free-piston Stirling cycles with silicon planar and GaAs concentrator photovoltaic power systems for application to missions beyond the Phase 2 Space Station level of technology for all power systems. Conceptual designs for Brayton and Stirling power systems were developed for 35 kWe and 7 kWe power levels. All power systems were designed for 7-year end-of-life conditions in low Earth orbit. LiF was selected for thermal energy storage for the solar dynamic systems. Results indicate that the Stirling cycle systems have the highest performance (lowest weight and area) followed by the Brayton cycle, with photovoltaic systems considerably lower in performance. For example, based on the performance assumptions used, the planar silicon power system weight was 55 to 75 percent higher than for the Stirling system. A technology program was developed to address areas wherein significant performance improvements could be realized relative to the current state-of-the-art as represented by Space Station. In addition, a preliminary evaluation of hardenability potential found that solar dynamic systems can be hardened beyond the hardness inherent in the conceptual designs of this study.

  16. Raman Line Imaging of Poly(ε-caprolactone)/Carbon Dioxide Solutions at High Pressures: A Combined Experimental and Computational Study for Interpreting Intermolecular Interactions and Free-Volume Effects.

    Pastore Carbone, Maria Giovanna; Musto, Pellegrino; Pannico, Marianna; Braeuer, Andreas; Scherillo, Giuseppe; Mensitieri, Giuseppe; Di Maio, Ernesto

    2016-09-01

    In the present study, a Raman line-imaging setup was employed to monitor in situ the CO2 sorption at elevated pressures (from 0.62 to 7.10 MPa) in molten PCL. The method allowed the quantitative measurement of gas concentration in both the time-resolved and the space-resolved modes. The combined experimental and theoretical approach allowed a molecular level characterization of the system. The dissolved CO2 was found to occupy a volume essentially coincident with its van der Waals volume and the estimated partial molar volume of the probe did not change with pressure. Lewis acid-Lewis base interactions with the PCL carbonyls was confirmed to be the main interaction mechanism. The geometry of the supramolecular complex and the preferential interaction site were controlled more by steric than electronic effects. On the basis of the indications emerging from Raman spectroscopy, an equation of state thermodynamic model for the PCL-CO2 system, based upon a compressible lattice fluid theory endowed with specific interactions, has been tailored to account for the interaction types detected spectroscopically. The predictions of the thermodynamic model in terms of molar volume of solution have been compared with available volumetric measurements while predictions for CO2 partial molar volume have been compared with the values estimated on the basis of Raman spectroscopy.

  17. Dynamic isotope studies in liver disease

    Weits, J

    1978-01-01

    Much information in the field of liver research has been gained by dynamic isotope studies. Clinically, these studies can help to settle selection criteria for different types of surgical shunt, which relieve the complications of portal hypertension. By performing splenoportoscintigraphy, splenic and portal vein thrombosis can be easily and safely excluded. So-called hypoxaemia of cirrhosis can most easily be diagnosed. Suprahepatic caval vein obstruction in a patient with cryptogenic liver disease is easily excluded by a radionuclide cavogram after injection of pertechnetate into a foot vein.

  18. Dynamics of Al/Fe{sub 2}O{sub 3} MIC combustion from short single-pulse photothermal initiation and time-resolved spectroscopy

    Stiegman, Albert E.; Park, Chi-Dong; Mileham, Melissa; Van de Burgt, Lambertus J. [Department of Chemistry and Biochemistry, Florida State University Tallahassee, FL (United States); Kramer, Michael P. [AFRL/MNME Eglin AFB, FL (United States)

    2009-08-15

    Time-resolved spectroscopy was used to study the dynamics of the photothermal ignition of Al/Fe{sub 2}O{sub 3} metastable intermolecular composites after single short-pulse laser initiation. The dynamics were recorded in several time domains from nanosecond to microsecond to quantify the dynamics from initial laser excitation to combustion. Time-averaged spectral data were also collected for the overall emission occurring during combustion. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  19. Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

    Ohara, Taku; Yuan, Tan Chia; Torii, Daichi; Kikugawa, Gota; Kosugi, Naohiro

    2011-07-21

    In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.

  20. Studies of network structure and dynamics of e-beam crosslinked PVPs. From macro to nano

    Dispenza, C.; Grimaldi, N.; Sabatino, M.A.; Todaro, S.; Alessi, S.; Spadaro, G.; Bulone, D.; Giacomazza, D.; Przybytniak, G.

    2011-01-01

    Complete text of publication follows. Much interest has been paid to develop a variety of radiation-crosslinked hydrated polymeric materials, which swell in water but do not dissolve, as biocompatible materials used for wound healing, drug delivery system, surface-coating material for medically used devices, etc. With the aim of establishing design rules to produce hydrogels of controlled size at the nanoscale and desired internal network structure using conventional electron accelerators and set-ups, here we attempt a description in terms of structural and dynamic properties of polymer networks generated through e-beam irradiation of aqueous solutions of the same model polymer, a commercial grade poly(N-vinyl-pyrrolidone), subjected to e-beam irradiation with a 12 MeV Linac accelerator, at same dose (40 kGy) and dose-rate (100 kGy/h) and at the variance of polymer concentration in water. Concentration has been systematically varied from above (10, 8, 6, 4, 2% w) to below (1, 0.5, 0.25, 0.1, 0.05% w) the critical chain overlap concentration value (∼ 1% w) of the chosen polymer in water, as estimated by intrinsic viscosity measurements. The transition between macroscopic gelation and micro-/nanogels formation is observed just below the critical overlap concentration (0.5% w), whereas the net prevalence of intra-molecular over inter-molecular crosslinking occurs at a polymer concentration below 0.25% w, as revealed by both dynamic and static laser light scattering measurements. Significant structural differences between nanoscalar 'finite' crosslinked networks and macrogels are evidenced by both FTIR and solid state NMR spectra. Polymeric segments mobility of the formed networks, at the different scales, has been assessed through stress-rheometry, solid-state cross-polarization times and nuclear relaxation time NMR studies of the freeze-dried residues.

  1. Intermolecular RNA Recombination Occurs at Different Frequencies in Alternate Forms of Brome Mosaic Virus RNA Replication Compartments

    Hernan Garcia-Ruiz

    2018-03-01

    Full Text Available Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to function as a preferred crossover site, but in order for individual RNAs to be recruited into the replication compartments. Moreover, modulating the form of the replication compartments from spherular vesicles (spherules to more expansive membrane layers increased intermolecular RNA recombination frequency by 200- to 1000-fold. We propose that intermolecular RNA recombination requires parental RNAs to be recruited into replication compartments as monomers, and that recruitment of multiple RNAs into a contiguous space is much more common for layers than for spherules. These results could explain differences in recombination frequencies between viruses that replicate in association with smaller spherules versus larger double-membrane vesicles and convoluted membranes.

  2. Rubrene: The interplay between intramolecular and intermolecular interactions determines the planarization of its tetracene core in the solid state

    Sutton, Christopher

    2015-06-15

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

  3. Molecular dynamics studies of actinide nitrides

    Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo

    2004-01-01

    The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)

  4. A dynamic approach to dependability studies

    Labeau, P.E.

    2008-01-01

    Dependability studies have now become an important part of the performance management of industrial plants. These last decades, several methods have been proposed and widely used for the analysis of systems of components subject to degradation and failure. These methods are based either on Boolean representations (for example, event trees/fault trees), or on discrete-state models (Markovian reliability, Petri nets, Bayesian networks...). However, the underlying, inherently continuous, physical processes have scarcely been accounted for, at least in an integrated fashion, in dependability studies. This paper first describes, through simple cases, the limitations of discrete approaches and the need of hybrid, discrete-continuous methods. It then summarizes the main concepts of dynamic reliability. Finally, some possible application domains are presented, as well as challenges that still need to be tackled to favour the diffusion of this approach among industrial circles. (author)

  5. Contribution to the study of dynamic recrystallization

    Guillope, Michel

    1981-01-01

    An experimental and theoretical work on dynamic recrystallization is presented. The experimental study, sustained by creep deformation of NaCl single crystals, has shown that the structural evolution can occur in two distinct ways: rotation recrystallization, which consists in a progressive sub-boundary misorientation increase; migration recrystallization, which consists in the 'catastrophic' growth of some grains. Although rotation recrystallization is to be observed for all experimental used conditions, migration recrystallization occurs only in a well defined domain of the temperature-applied stress-impurity concentration space. The proposed interpretation emphasizes the generality of the observed behaviours: the sharp boundary of the migration recrystallization domain expresses the existence of a 'catastrophic' transition from a low velocity regime (boundaries migrate charged with segregate impurities) to a high velocity regime (boundaries migrate free from impurities). Owing to the importance of grain boundary migration in dynamic recrystallization, a detailed analysis of possible migration mechanisms is presented: we show how migration induced by applied stress or recrystallization force can be explained. Finally, an original kinetic model of grain growth is developed which throws a new insight in the abnormal grain growth process and, by analogy, in the migration recrystallization phenomenon. (author) [fr

  6. Molecular beam studies of reaction dynamics

    Lee, Yuan T.

    1991-03-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation

  7. Ultrasonic Study of Dislocation Dynamics in Lithium -

    Han, Myeong-Deok

    1987-09-01

    Experimental studies of dislocation dynamics in LiF single crystals, using ultrasonic techniques combined with dynamic loading, were performed to investigate the time evolution of the plastic deformation process under a short stress pulse at room temperature, and the temperature dependence of the dislocation damping mechanism in the temperature range 25 - 300(DEGREES)K. From the former, the time dependence of the ultrasonic attenuation was understood as resulting from dislocation multiplication followed by the evolution of mobile dislocations to immobile ones under large stress. From the latter, the temperature dependence of the ultrasonic attenuation was interpreted as due to the motion of the dislocation loops overcoming the periodic Peierls potential barrier in a manner analogous to the motion of a thermalized sine-Gordon chain under a small stress. The Peierls stress obtained from the experimental results by application of Seeger's relaxation model with exponential dislocation length distribution was 4.26MPa, which is consistent with the lowest stress for the linear relation between the dislocation velocity and stress observed by Flinn and Tinder.

  8. Experimental study of vapor bubble dynamics

    Pasquini, Maria-Elena

    2015-01-01

    The object of this thesis is an experimental study of vapor bubble dynamics in sub-cooled nucleate boiling. The test section is locally heated by focusing a laser beam: heat fluxes from 1 e4 to 1.5 e6 W/m 2 and water temperature between 100 and 88 C have been considered. Three boiling regimes have been observed. Under saturated conditions and with low heat fluxes a developed nucleate boiling regime has been observed. Under higher sub-cooling and still with low heat fluxes an equilibrium regime has been observed in which the liquid flowrate evaporating at the bubble base is compensated by the vapor condensing flowrate at bubble top. A third regime have been observed at high heat fluxes for all water conditions: it is characterized by the formation of a large dry spot on the heated surface that keeps the nucleation site dry after bubble detachment. The condensation phase starts after bubble detachment. Bubble equivalent radius at detachment varies between 1 and 2.5 mm. Bubble properties have been measured and non-dimensional groups have been used to characterize bubble dynamics. Capillary waves have been observed on the bubble surface thanks to high-speed images acquisition. Two main phenomena have been proposed to explain capillary waves effects on bubble condensation: increasing of the phases interface area and decreasing of vapor bubble translation velocity, because of the increased drag force on the deformed bubble. (author) [fr

  9. Molecular beam studies of reaction dynamics

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  10. Intermolecular interactions of decamethoxinum and acetylsalicylic acid in systems of various complexity levels

    O. V. Vashchenko

    2016-07-01

    Full Text Available Intermolecular interactions between decamethoxinum (DEC and acetylsalicylic acid (ASА have been studied in the phospholipid-containing systems of escalating complexity levels. The host media for these substances were solvents, L-α-dipalmitoylphosphatidylcholine (DPPC membranes, and samples of human erythrocytes. Peculiar effects caused by DEC-ASА interaction have been observed in each system using appropriate techniques: (a DEC-ASА non-covalent complexes formation in DPPC-containing systems were revealed by mass spectrometry with electrospray ionization; (b joint DEC-ASА action on DPPC model membranes led to increasing of membrane melting temperature Tm, whereas individual drugs caused pronounced Tm decreasing, which was demonstrated by differential scanning calorimetry; (c deceleration of DEC-induced haemolysis of erythrocytes under joint DEC-ASА application was observed by optical microscopy.

  11. Dielectric behaviour and intermolecular association between L(+) ascorbic acid and ethanol

    Rudyk, R.A.; Torres, M.C.; Acuna Molina, M.A.

    1990-01-01

    In order to determine the dipole moment of L(+) ascorbic acid and the relation to its structure the experimental variations of permitivities, refractive indices and specific volumes of a series of dilute ethanolic solutions at 25 deg C were examined. The average moment (μ) using Buckingham equation was found to be 5,58 D considering the spherical approximation and 7,81 D if the ellipsoidal form factor was considered. The calculated μ value through vectorial addition was 4,98 D. The solute partial molal volume in the studied range was calculated to be 94,73 cm 3 instead of the theoretical value of 106,71 cm 3 . Both discrepancies are attributed to intermolecular solute-solvent interactions. A possible electronic displacement which favours hydrogen bonding with the solvent is postulated. (Author) [es

  12. Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (DiaminocarbenePdII Complexes

    Alexander S. Mikherdov

    2018-02-01

    Full Text Available The coupling of cis-[PdCl2(CNXyl2] (Xyl = 2,6-Me2C6H3 with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbenePdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB. The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D polymeric chains (for 3a,b, dimeric associates (for 3c, or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%, S•••S (3c: less 1%, S•••O (3d: less 1%. The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method, confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry. The AIM analysis demonstrates the presence of appropriate bond critical points for these

  13. Rewetting phenomena and their relation to intermolecular forces between a hot wall and the fluid

    Gerweck, V.

    1989-12-01

    The rewetting phenomena and the different physical concepts which are used in their modelisation are reviewed. The present work studies the effect of the intermolecular forces between the hot wall and the fluid on this phase transition. Using suitable approximations, a local equation of state is obtained by the treatment of the fluid-fluid and fluid-wall intermolecular interactions. This local equation of state depends on the distance from the wall, and the critical pressure and temperature become a function of the distance from the wall, whereas the critical density is left constant throughout the fluid. At the wall, the critical pressure and temperature are half their bulk values and increase towards the bulk value as the distance from the wall increases. The penetration of a temperature profile in this fluid is studied by assuming that the liquid density is not strongly affected by this temperature profile as long as there is no phase transition. It is shown that the phase transition will occur extremely rapidly when the interfacial temperature upon contact is higher than the minimum of the local spinodal temperature, which varies with the distance from the wall. The result ist cast in the form of an interfacial rewetting temperature fT c above which rewetting of the surface by liquid-wall contacts is not expected because these contacts will be terminated in extremely short times. Comparing the theory with available data shows that in the usual rewetting situations the theory reduces to the use of the bulk spinodal temperature. For surfaces coated with poorly wetted materials the correction factor due to surface effects applies, reducing the rewetting temperature, in agreement with the experimental data. For liquid metals it appears that the theory is applied in a region where the basic theoretical approximations are very coarse; but even in that case the experimental trend is qualitatively predicted by the theory. (author) 43 figs., 11 tabs., 105 refs

  14. Localized-overlap approach to calculations of intermolecular interactions

    Rob, Fazle

    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.

  15. Molecular dynamic simulation study of molten cesium

    Yeganegi Saeid

    2017-01-01

    Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

  16. Non Linear Beam Dynamics Studies at SPEAR

    Terebilo, A.; Pellegrini, C.; Cornacchia, M.; Corbett, J.; Martin, D.

    2011-01-01

    The frequency map analysis of a Hamiltonian system recently introduced to accelerators physics in combination with turn-by-turn phase space measurements opens new experimental opportunities for studying non linear dynamic in storage rings. In this paper we report on the experimental program at SPEAR having the goal of measuring the frequency map of the machine. In this paper we discuss the accuracy of the instantaneous tune extraction from experimental data and demonstrate the possibility of the frequency map measurement. The instantaneous tune extraction technique can be applied to experimental tracking data with reasonable accuracy. Frequency map can be experimentally determined using the existing turn-by-turn phase space measurement techniques and NAFF instantaneous tune extraction.

  17. Theoretical study of fission dynamics with muons

    Oberacker, V.E.; Umar, A.S.; Bottcher, C.; Strayer, M.R.; Maruhn, J.A.; Frankfurt Univ.

    1992-01-01

    Following muon capture by actinide atoms, some of the inner shell muonic transitions proceed by inverse internal conversion, i.e. the excitation energy of the muonic atom is transferred to the nucleus. In particular, the muonic E2:(3d→1s) transition energy is close to the peak of the isoscalar giant quadrupole resonance in actinide nuclei which exhibits a large fission width. Prompt fission in the presence of a bound muon allows us to study the dynamics of large-amplitude collective motion. We solve the time-dependent Dirac equation for the muonic spinor wave function in the Coulomb field of the fissioning nucleus on a 3-dimensional lattice and demonstrate that the muon attachment probability to the light fission fragment is a measure of the nuclear energy dissipation between the outer fission barrier and the scission point

  18. Radionuclide renal dynamic and function study

    Guan Liang

    1991-01-01

    The radionuclide dynamic and function study, glomerular filtration rate (GFR) and effective renal plasma flow (ERPF) were reported in 14 cases of renal and ureteral calculi patients before and after extracorporeal shock wave lithotripsy (ESWL). In 12 cases with normal renal blood flow, within 3 months after ESWL, the GFR of shock and non-shock side decreased with different extent, while the individual ERPF had little change. In 5 cases followed up 1 year after ESWL, the individual GFR and ERPF were normal. In 2 cases of severe renal function insufficiency, there was no improvement in renal function in shock side, after 5 months and 1 year, the renal function was still at low level. Thereby it is considered that ESWL is not suitable for the renal calculi patients with severe renal function insufficiency

  19. Orientation correlation and intermolecular structure of GeCl4, VCl4 and other tetrachloride liquids

    Nath, P.P.; Sarkar, S.; Joarder, R.N.

    2007-01-01

    The intermolecular structure and correlation of GeCl 4 , VCl 4 and other tetrachloride liquids can be well described by Misawa's orientation correlation model originally applied to liquid CCl 4 . The model supports on average a specific 'corner' to 'face' correlation, but evidently very different from 'Apollo' type model. The Misawa model appears to work, in some respect, even better than reference interaction site model (RISM) used for long to describe intermolecular structure of such molecular systems. The test and comparison are made through the calculation of small asymmetric part of the intermolecular structure and evaluation of partial atom-atom distribution functions

  20. Molecular beam studies of adsorption dynamics

    Arumainayagam, C.R.; McMaster, M.C.; Madix, R.J.

    1991-01-01

    We have investigated the trapping dynamics of C 1 -C 3 alkanes and Xe on Pt(111) using supersonic molecular beams and a direct technique to measure trapping probabilities. We have extended a one-dimensional model based on classical mechanics to include trapping and have found semiquantitative agreement with experimental results for the dependence of the initial trapping probability on incident translational energy at normal incidence. Our measurements of the initial trapping probability as a function of incident translational energy at normal incidence are in agreement with previous mean translational energy measurements for Xe and CH 4 desorbing near the surface normal, in accordance with detailed balance. However, the angular dependence of the initial trapping probability shows deviations from normal energy scaling, demonstrating the importance of parallel momentum in the trapping process and the inadequacy of one-dimensional models. The dependence of the initial trapping probability of Xe on incident translational energy and angle is quite well fit by three-dimensional stochastic classical trajectory calculations utilizing a Morse potential. Angular distributions of the scattered molecules indicate that the trapping probability is not a sensitive function of surface temperature. The trapping probability increases with surface coverage in quantitative agreement with a modified Kisliuk model which incorporates enhanced trapping onto the monolayer. We have also used the direct technique to study trapping onto a saturated monolayer state to investigate the dynamics of extrinsic precursor adsorption and find that the initial trapping probability onto the monolayer is higher than on the clean surface. The initial trapping probability onto the monolayer scales with total energy, indicating a highly corrugated interaction potential

  1. Systems-Dynamic Analysis for Neighborhood Study

    Systems-dynamic analysis (or system dynamics (SD)) helps planners identify interrelated impacts of transportation and land-use policies on neighborhood-scale economic outcomes for households and businesses, among other applications. This form of analysis can show benefits and tr...

  2. Intermolecular interaction of fosinopril with bovine serum albumin (BSA): The multi-spectroscopic and computational investigation.

    Zhou, Kai-Li; Pan, Dong-Qi; Lou, Yan-Yue; Shi, Jie-Hua

    2018-04-16

    The intermolecular interaction of fosinopril, an angiotensin converting enzyme inhibitor with bovine serum albumin (BSA), has been investigated in physiological buffer (pH 7.4) by multi-spectroscopic methods and molecular docking technique. The results obtained from fluorescence and UV absorption spectroscopy revealed that the fluorescence quenching mechanism of BSA induced by fosinopril was mediated by the combined dynamic and static quenching, and the static quenching was dominant in this system. The binding constant, K b , value was found to lie between 2.69 × 10 3 and 9.55 × 10 3  M -1 at experimental temperatures (293, 298, 303, and 308 K), implying the low or intermediate binding affinity between fosinopril and BSA. Competitive binding experiments with site markers (phenylbutazone and diazepam) suggested that fosinopril preferentially bound to the site I in sub-domain IIA on BSA, as evidenced by molecular docking analysis. The negative sign for enthalpy change (ΔH 0 ) and entropy change (ΔS 0 ) indicated that van der Waals force and hydrogen bonds played important roles in the fosinopril-BSA interaction, and 8-anilino-1-naphthalenesulfonate binding assay experiments offered evidence of the involvements of hydrophobic interactions. Moreover, spectroscopic results (synchronous fluorescence, 3-dimensional fluorescence, and Fourier transform infrared spectroscopy) indicated a slight conformational change in BSA upon fosinopril interaction. Copyright © 2018 John Wiley & Sons, Ltd.

  3. Analysis of intermolecular RNA-RNA recombination by rubella virus

    Adams, Sandra D.; Tzeng, W.-P.; Chen, M.-H.; Frey, Teryl K.

    2003-01-01

    To investigate whether rubella virus (RUB) undergoes intermolecular RNA-RNA recombination, cells were cotransfected with pairs of in vitro transcripts from genomic cDNA plasmid vectors engineered to contain nonoverlapping deletions: the replicative transcript maintained the 5'-proximal nonstructural (NS) ORF (which contained the replicase, making it RNA replication competent), had a deletion in the 3'-proximal structural protein (SP) ORF, and maintained the 3' end of the genome, including the putative 3' cis-acting elements (CSE), while the nonreplicative transcript consisted of the 3' half of the genome including the SP-ORF and 3' CSE. Cotransfection yielded plaque-forming virus that synthesized the standard genomic and subgenomic RNAs and thus was generated by RNA-RNA recombination. Using transcripts tagged with a 3'-terminal deletion, it was found that recombinants contained the 3' end derived from the replicative strand, indicating a cis-preference for initiation of negative-strand synthesis. In cotransfections in which the replicative transcript lacked the 3' CSE, recombination occurred, albeit at lower efficiency, indicating that initiation in trans from the NS-ORF can occur. The 3' CSE was sufficient as a nonreplicative transcript, showing that it can serve as a promoter for negative-strand RNA synthesis. While deletion mutagenesis showed that the presence of the junction untranslated region (J-UTR) between the ORFs appeared to be necessary on both transcripts for recombination in this region of the genome, analysis with transcripts tagged with restriction sites showed that the J-UTR was not a hot spot for recombination compared to neighboring regions in both ORFs. Sequence analysis of recombinants revealed that both precise (homologous) and imprecise recombination (aberrant, homologous resulting in duplications) occurred; however, imprecise recombination only involved the J-UTR or the 3' end of the NS-ORF and the J-UTR (maintaining the NS-ORF), indicating

  4. Exciplex: An Intermolecular Charge-Transfer Approach for TADF.

    Sarma, Monima; Wong, Ken-Tsung

    2018-04-03

    Organic materials that display thermally activated delayed fluorescence (TADF) are a striking class of functional materials that have witnessed a booming progress in recent years. In addition to pure TADF emitters achieved by the subtle manipulations of intramolecular charge transfer processes with sophisticated molecular structures, a new class of efficient TADF-based OLEDs with emitting layer formed by blending electron donor and acceptor molecules that involve intermolecular charge transfer have also been fabricated. In contrast to pure TADF materials, the exciplex-based systems can realize small ΔEST (0-0.05 eV) much more easily since the electron and hole are positioned on two different molecules, thereby giving small exchange energy. Consequently, exciplex-based OLEDs have the prospective to maximize the TADF contribution and achieve theoretical 100% internal quantum efficiency. Therefore, the challenging issue of achieving small ΔEST in organic systems could be solved. In this article, we summarize and discuss the latest and most significant developments regarding these rapidly evolving functional materials, wherein the majority of the reported exciplex forming systems are categorized into two sub-groups, viz. (a) exciplex as TADF emitters and (b) those as hosts for fluorescent, phosphorescent and TADF dopants according to their structural features and applications. The working mechanisms of the direct electroluminescence from the donor/acceptor interface and the exciplex-forming systems as co-host for the realization of high efficiency OLEDs are reviewed and discussed. This article delivers a summary of the current progresses and achievements of exciplex-based researches and points out the future challenges to trigger more research endeavors to this growing field.

  5. Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study.

    Urbanc, B; Betnel, M; Cruz, L; Bitan, G; Teplow, D B

    2010-03-31

    Oligomers of amyloid beta-protein (Abeta) play a central role in the pathology of Alzheimer's disease. Of the two predominant Abeta alloforms, Abeta(1-40) and Abeta(1-42), Abeta(1-42) is more strongly implicated in the disease. We elucidated the structural characteristics of oligomers of Abeta(1-40) and Abeta(1-42) and their Arctic mutants, [E22G]Abeta(1-40) and [E22G]Abeta(1-42). We simulated oligomer formation using discrete molecular dynamics (DMD) with a four-bead protein model, backbone hydrogen bonding, and residue-specific interactions due to effective hydropathy and charge. For all four peptides under study, we derived the characteristic oligomer size distributions that were in agreement with prior experimental findings. Unlike Abeta(1-40), Abeta(1-42) had a high propensity to form paranuclei (pentameric or hexameric) structures that could self-associate into higher-order oligomers. Neither of the Arctic mutants formed higher-order oligomers, but [E22G]Abeta(1-40) formed paranuclei with a similar propensity to that of Abeta(1-42). Whereas the best agreement with the experimental data was obtained when the charged residues were modeled as solely hydrophilic, further assembly from spherical oligomers into elongated protofibrils was induced by nonzero electrostatic interactions among the charged residues. Structural analysis revealed that the C-terminal region played a dominant role in Abeta(1-42) oligomer formation whereas Abeta(1-40) oligomerization was primarily driven by intermolecular interactions among the central hydrophobic regions. The N-terminal region A2-F4 played a prominent role in Abeta(1-40) oligomerization but did not contribute to the oligomerization of Abeta(1-42) or the Arctic mutants. The oligomer structure of both Arctic peptides resembled Abeta(1-42) more than Abeta(1-40), consistent with their potentially more toxic nature.

  6. Catalytic Intermolecular Cross-Couplings of Azides and LUMO-Activated Unsaturated Acyl Azoliums

    Li, Wenjun; Ajitha, Manjaly John; Lang, Ming; Huang, Kuo-Wei; Wang, Jian

    2017-01-01

    An example for the catalytic synthesis of densely functionalized 1,2,3-triazoles through a LUMO activation mode has been developed. The protocol is enabled by intermolecular cross coupling reactions of azides with in situ-generated alpha

  7. The Raman and vibronic activity of intermolecular vibrations in aromatic-containing complexes and clusters

    Maxton, P.M.; Schaeffer, M.W.; Ohline, S.M.; Kim, W.; Venturo, V.A.; Felker, P.M.

    1994-01-01

    Theoretical and experimental results pertaining to the excitation of intermolecular vibrations in the Raman and vibronic spectra of aromatic-containing, weakly bound complexes and clusters are reported. The theoretical analysis of intermolecular Raman activity is based on the assumption that the polarizability tensor of a weakly bound species is given by the sum of the polarizability tensors of its constituent monomers. The analysis shows that the van der Waals bending fundamentals in aromatic--rare gas complexes may be expected to be strongly Raman active. More generally, it predicts strong Raman activity for intermolecular vibrations that involve the libration or internal rotation of monomer moieties having appreciable permanent polarizability anisotropies. The vibronic activity of intermolecular vibrations in aromatic-rare gas complexes is analyzed under the assumption that every vibronic band gains its strength from an aromatic-localized transition. It is found that intermolecular vibrational excitations can accompany aromatic-localized vibronic excitations by the usual Franck--Condon mechanism or by a mechanism dependent on the librational amplitude of the aromatic moiety during the course of the pertinent intermolecular vibration. The latter mechanism can impart appreciable intensity to bands that are forbidden by rigid-molecule symmetry selection rules. The applicability of such rules is therefore called into question. Finally, experimental spectra of intermolecular transitions, obtained by mass-selective, ionization-detected stimulated Raman spectroscopies, are reported for benzene--X (X=Ar, --Ar 2 , N 2 , HCl, CO 2 , and --fluorene), fluorobenzene--Ar and --Kr, aniline--Ar, and fluorene--Ar and --Ar 2 . The results support the conclusions of the theoretical analyses and provide further evidence for the value of Raman methods in characterizing intermolecular vibrational level structures

  8. Intermolecular failure of L-type Ca2+ channel and ryanodine receptor signaling in hypertrophy.

    Ming Xu

    2007-02-01

    Full Text Available Pressure overload-induced hypertrophy is a key step leading to heart failure. The Ca(2+-induced Ca(2+ release (CICR process that governs cardiac contractility is defective in hypertrophy/heart failure, but the molecular mechanisms remain elusive. To examine the intermolecular aspects of CICR during hypertrophy, we utilized loose-patch confocal imaging to visualize the signaling between a single L-type Ca(2+ channel (LCC and ryanodine receptors (RyRs in aortic stenosis rat models of compensated (CHT and decompensated (DHT hypertrophy. We found that the LCC-RyR intermolecular coupling showed a 49% prolongation in coupling latency, a 47% decrease in chance of hit, and a 72% increase in chance of miss in DHT, demonstrating a state of "intermolecular failure." Unexpectedly, these modifications also occurred robustly in CHT due at least partially to decreased expression of junctophilin, indicating that intermolecular failure occurs prior to cellular manifestations. As a result, cell-wide Ca(2+ release, visualized as "Ca(2+ spikes," became desynchronized, which contrasted sharply with unaltered spike integrals and whole-cell Ca(2+ transients in CHT. These data suggested that, within a certain limit, termed the "stability margin," mild intermolecular failure does not damage the cellular integrity of excitation-contraction coupling. Only when the modification steps beyond the stability margin does global failure occur. The discovery of "hidden" intermolecular failure in CHT has important clinical implications.

  9. Observation of aggregation triggered by Resonance Energy Transfer (RET) induced intermolecular pairing force.

    Pan, Xiaoyong; Wang, Weizhi; Ke, Lin; Zhang, Nan

    2017-07-20

    In this report, we showed the existence of RET induced intermolecular pairing force by comparing their fluorescence behaviors under room illumination vs standing in dark area for either PFluAnt solution or PFluAnt&PFOBT mixture. Their prominent emission attenuation under room illumination brought out the critical role of photo, i.e. RET induced intermolecular pairing force in induction of polymer aggregation. Constant UV-Vis absorption and fluorescence spectra in terms of both peak shapes and maximum wavelengths implied no chemical decomposition was involved. Recoverable fluorescence intensity, fluorescence lifetime as well as NMR spectra further exclude photo induced decomposition. The controllable on/off state of RET induced intermolecular pairing force was verified by the masking effect of outside PFluAnt solution which function as filter to block the excitation of inside PFluAnt and thus off the RET induced intermolecular pairing force. Theoretical calculation suggest that magnitude of RET induced intermolecular pairing force is on the same scale as that of van der Waals interaction. Although the absolute magnitude of RET induced intermolecular pairing force was not tunable, its effect can be magnified by intentionally turn it "on", which was achieved by irradiance with 5 W desk lamp in this report.

  10. Dielectric dispersion, relaxation dynamics and thermodynamic studies of Beta-Alanine in aqueous solutions using picoseconds time domain reflectometry

    Vinoth, K.; Ganesh, T.; Senthilkumar, P.; Sylvester, M. Maria; Karunakaran, D. J. S. Anand; Hudge, Praveen; Kumbharkhane, A. C.

    2017-09-01

    The aqueous solution of beta-alanine characterised and studied by their dispersive dielectric properties and relaxation process in the frequency domain of 10×106 Hz to 30×109 Hz with varying concentration in mole fractions and temperatures. The molecular interaction and dielectric parameters are discussed in terms of counter-ion concentration theory. The static permittivity (ε0), high frequency dielectric permittivity (ε∞) and excess dielectric parameters are accomplished by frequency depended physical properties and relaxation time (τ). Molecular orientation, ordering and correlation factors are reported as confirmation of intermolecular interactions. Ionic conductivity and thermo dynamical properties are concluded with the behaviour of the mixture constituents. Solute-solvent, solute-solute interaction, structure making and breaking abilities of the solute in aqueous medium are interpreted. Fourier Transform Infrared (FTIR) spectra of beta- alanine single crystal and liquid state have been studied. The 13C Nuclear Magnetic Resonance (NMR) spectral studies give the signature for resonating frequencies and chemical shifts of beta-alanine.

  11. Molecular dynamics studies of superionic conductors

    Rahman, A.

    1979-01-01

    Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard

  12. Prolactin secretion: the impact of dynamic studies

    L'Hermite, M.; Degueldre, M.; Caufriez, A.; Delvoye, P.; Robyn, C.

    1975-01-01

    Human prolactin blood levels were determined by radioimmunoassay in basal condition and in response to various inhibiting and/or stimulating agents (levodopa, water overload, insulinic hypoglycaemia, synthetic TRH, sulpiride) in cases of disturbed hypothalamo-pituitary axis (failure to lactate, prolactin-secreting pituitary adenomas, acromegaly, other pituitary tumours, clinical panhypopituitarism). A blunted prolactin response to suckling was evidenced in 2 post-partum women who were unable to breast feed. Hyperprolactinaemia, whether related to the existence of a prolactin-producing adenoma or not was associated with the disappearance of the normal circadian pattern of prolactin secretion and with a blunted relative response to TRH; the latter phenomenon occurred also in acromegaly regardless of the basal prolactinaemia, and during the last trimester of pregnancy. Water overload was unsuccessful to suppress prolactin during the last trimester of pregnancy while the acute administration of levodopa was quite effective in about half of the patients with pituitary tumour. Therefore none of the dynamic tests presently studied allowed to attribute a hyperprolactinaemia to a pituitary tumour rather than to a functional disturbance. On the contrary, stimulation tests can help to locate the level of a defect in cases of hypopituitarism [fr

  13. Thermal transpiration: A molecular dynamics study

    T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  14. Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

    Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

    2018-05-01

    Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

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

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

    2015-12-01

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

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

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

    2010-07-29

    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

  17. New models for intermolecular repulsion and their application to Van Der Waals complexes and crystals of organic molecules

    Tsui, H.H.Y.

    2001-01-01

    Model intermolecular potentials are required for simulations of molecules in the gas, liquid, or solid phase. The widely used isotropic atom-atom model potentials are empirically fitted and based on the assumptions of transferability, combining rules and that atoms in molecules are spherical. This thesis develops a non-empirical method of modelling repulsion by applying the overlap model, which we show as a general non-empirical method of deriving repulsion potentials for a specific molecule. In this thesis, the repulsion parameters for an exponential atom-atom model potential are obtained from the ab initio charge density of a small organic molecule by making the assumption that the repulsion is proportional to the overlap of a pair of molecules. The proportionality constant is fixed by a limited number of intermolecular perturbation theory (IMPT) calculations. To complete the model potential, the electrostatic interaction is represented by a distributed multipole analysis, and the Slater-Kirkwood formula is used for the dispersion. These non-empirical potentials can reproduce experimental crystal structure when applied to crystal structure prediction of an oxyboryl derivative. A detailed study on further improving the overlap model was carried out for phenol-water, by including other minor intermolecular contributions of charge-transfer and penetration. High quality ab initio calculations on the complex were performed for use in comparison. To compare with experimental data, diffusion Monte Carlo simulations were performed with the potential, so that the effects of anharmonic zero-point motion on structure and energy of the system are included. When the system is too large for an IMPT calculation, the proportionality constant can be determined empirically by fitting the cell volume as shown in our study of crystal structures of chlorothalonil. This is used with an anisotropic repulsion model that has been derived for Cl and N atoms in chlorothalonil. This model

  18. Final report for NIF chamber dynamics studies

    Burnham, A; Peterson, P F; Scott, J M

    1998-01-01

    The National Ignition Facility (NIF), a 1.8 MJ, 192 laser beam facility, will have anticipated fusion yields of up to 20 MJ from D-T pellets encased in a gold hohlraum target. The energy emitted from the target in the form of x rays, neutrons, target debris kinetic energy, and target shrapnel will be contained in a 5 m. radius spherical target chamber. various diagnostics will be stationed around the target at varying distances from the target. During each shot, the target will emit x rays that will vaporize nearby target facing surfaces including those of the diagnostics, the target positioner, and other chamber structures. This ablated vapor will be transported throughout the chamber, and will eventually condense and deposit on surfaces in the chamber, including the final optics debris shields. The research at the University of California at Berkeley relates primarily to the NIF chamber dynamics. The key design issues are the ablation of the chamber structures, transport of the vapor through the chamber and the condensation or deposition processes of those vaporized materials. An understanding of these processes is essential in developing a concept for protecting the fina optics debris shields from an excessive coating (> 10 A) of target debris and ablated material, thereby prolonging their lifetime between change-outs. At Berkeley, we have studied the physical issues of the ablation process and the effects of varying materials, the condensation process of the vaporized material, and design schemes that can lower the threat posed to the debris shields by these processes. The work or portions of the work completed this year have been published in several papers and a dissertation [l-5

  19. Dynamics in Complex Coacervates

    Perry, Sarah

    Understanding the dynamics of a material provides detailed information about the self-assembly, structure, and intermolecular interactions present in a material. While rheological methods have long been used for the characterization of complex coacervate-based materials, it remains a challenge to predict the dynamics for a new system of materials. Furthermore, most work reports only qualitative trends exist as to how parameters such as charge stoichiometry, ionic strength, and polymer chain length impact self-assembly and material dynamics, and there is little information on the effects of polymer architecture or the organization of charges within a polymer. We seek to link thermodynamic studies of coacervation phase behavior with material dynamics through a carefully-controlled, systematic study of coacervate linear viscoelasticity for different polymer chemistries. We couple various methods of characterizing the dynamics of polymer-based complex coacervates, including the time-salt superposition methods developed first by Spruijt and coworkers to establish a more mechanistic strategy for comparing the material dynamics and linear viscoelasticity of different systems. Acknowledgment is made to the Donors of the American Chemical Society Petroleum Research Fund for support of this research.

  20. Raman spectroscopic study of reaction dynamics

    MacPhail, R. A.

    1990-12-01

    The Raman spectra of reacting molecules in liquids can yield information about various aspects of the reaction dynamics. The author discusses the analysis of Raman spectra for three prototypical unimolecular reactions, the rotational isomerization of n-butane and 1,2-difluoroethane, and the barrierless exchange of axial and equatorial hydrogens in cyclopentane via pseudorotation. In the first two cases the spectra are sensitive to torsional oscillations of the gauche conformer, and yield estimates of the torsional solvent friction. In the case of cyclopentane, the spectra can be used to discriminate between different stochastic models of the pseudorotation dynamics, and to determine the relevant friction coefficients.

  1. Interplay between intramolecular and intermolecular structures of 1,1,2,2-tetrachloro-1,2-difluoroethane

    Rovira-Esteva, M.; Murugan, N. A.; Pardo, L. C.; Busch, S.; Tamarit, J. Ll.; Pothoczki, Sz.; Cuello, G. J.; Bermejo, F. J.

    2011-08-01

    We report on the interplay between the short-range order of molecules in the liquid phase of 1,1,2,2-tetrachloro-1,2-difluoroethane and the possible molecular conformations, trans and gauche. Two complementary approaches have been used to get a comprehensive picture: analysis of neutron-diffraction data by a Bayesian fit algorithm and a molecular dynamics simulation. The results of both show that the population of trans and gauche conformers in the liquid state can only correspond to the gauche conformer being more stable than the trans conformer. Distinct conformer geometries induce distinct molecular short-range orders around them, suggesting that a deep intra- and intermolecular interaction coupling is energetically favoring one of the conformers by reducing the total molecular free energy.

  2. Dynamic Aperture Studies for SPEAR 3

    Nosochkov, Yuri

    1999-01-01

    The SSRL is investigating an accelerator upgrade project to replace the present 130 nm.rad FODO lattice with an 18 nm.rad double bend achromat lattice: SPEAR 3. In this paper, we review the methods used to maximize the SPEAR 3 dynamic aperture including optimization of linear optics, betatron tune, chromaticity and coupling correction, and effects of machine errors and insertion devices

  3. Excess water dynamics in hydrotalcite: QENS study

    dynamics of excess water in hydrotalcite sample with varied content of excess water are reported. Translational motion of excess water can be best described by random transla- tional jump diffusion model. The observed increase in translational diffusivity with increase in the amount of excess water is attributed to the ...

  4. Dynamic Aperture Studies for SPEAR 3

    Corbett, William

    1998-01-01

    The Stanford Synchrotron Radiation Laboratory is investigating an accelerator upgrade project that would replace the present 130 nm rad FODO lattice with an 18 nm rad double bend achromat (DBA) lattice: SPEAR 3. The low emittance design yields a high brightness beam, but the stronger focusing in the DBA lattice increases chromaticity and beam sensitivity to machine errors. To ensure efficient injection and long Touschek lifetime, an optimization of the design lattice and dynamic aperture has been performed. In this paper, we review the methods used to maximize the SPEAR 3 dynamic aperture including necessary optics modifications, choice of tune and phase advance, optimization of sextupole and coupling correction, and modeling effects of machine errors, wigglers and lattice periodicity

  5. Dynamic aperture studies for SPEAR 3

    Nosochkov, Y.; Corbett, J.

    1999-01-01

    The Stanford Synchrotron Radiation Laboratory is investigating an accelerator upgrade project that would replace the present 130 nm·rad FODO lattice with an 18 nm·rad double bend achromat (DBA) lattice: SPEAR 3. The low emittance design yields a high brightness beam, but the stronger focusing in the DBA lattice increases chromaticity and beam sensitivity to machine errors. To ensure efficient injection and long Touschek lifetime, an optimization of the design lattice and dynamic aperture has been performed. In this paper, we review the methods used to maximize the SPEAR 3 dynamic aperture including necessary optics modifications, choice of tune and phase advance, optimization of sextupole and coupling correction, and modeling effects of machine errors, wigglers and lattice periodicity

  6. Sensitivity case study in dynamic reliability

    Kopustinskas, V.

    2001-01-01

    Recent trends in the risk assessments of the complex industrial plants show increased interest in dynamical models arising from the coupling of the probabilistic and deterministic approaches. Conventionally used static system models, represented by the fault/event trees can not reflect dynamic behaviour of the system and complex interaction between the process variables, components and human actions. The nature of the most complex industrial systems, like nuclear power plants (NPP) suggests that Markov type stochastic differential equations (SDEs) consisting of jump and drift components can be successfully used to represent and analyze the phenomena. This paper discuss possible applications of the SDEs in reliability problems. In particular, Accident Localization System (ALS) of the Ignalina NPP was analyzed as a benchmark for further investigations in this area. (author)

  7. Application of iterative reconstruction in dynamic studies

    Meikle, S.R.

    1998-01-01

    Full text: The conventional approach to analysing dynamic tomographic data (SPECT or PET) is to reconstruct projections corresponding to each time interval separately and then fit a suitable tracer kinetic model to the dynamic sequence (method 1 ) . This approach assumes that the tracer distribution remains static during any given time interval and, for practical reasons, filtered back-projection (FBP) is the preferred reconstruction algorithm. However, alternative approaches exist which lend themselves to iterative algorithms, such as EM. One approach is to fit the model directly to the projection data, followed by EM reconstruction of the parameter estimates (method 2). This requires that the tracer model can be expressed as a linear function of the unknown model parameters. A third alternative is to incorporate the tracer model into the reconstruction algorithm (method 3). Such an extension was described during the early development of the EM algorithm, referred to as the EM parametric image reconstruction algorithm (EM-PIRA). We have investigated these various strategies for analysing dynamic data and their relative pros and cons. Tracer modelling was performed using a general model, referred to as spectral analysis, which makes no restriction on the number of physiological compartments and satisfies the linearity requirement of method 2. A kinetic software phantom was created and used to test the convergence and noise properties of the different approaches. In summary, method 2 is the most practical as it reduces the number of reconstructions by at least an order of magnitude and provides improved signal-to-noise ratios compared with method 1. EM-PIRA allows greater flexibility in the choice of parametric images and appears to have a regularising effect on convergence. Methods 2 and 3 are also better suited to dynamic scanning with a rotating camera, as they can potentially account for changes in tracer distribution between projections

  8. Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

    Elena ePapaleo

    2015-05-01

    Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  9. A dynamical study on extrasolar comets

    Loibnegger, B.; Dvorak, R.

    2017-09-01

    Since the detection of absorption features in spectra of beta Pictoris varying on short time scales it is known that comets exist in other stellar systems. We investigate the dynamics of comets in two differently build systems (HD 10180 and HIP 14810). The outcomes of the scattering process, as there are collisions with the planets, captures and ejections from the systems are analysed statistically. Collisions and close encounters with the planets are investigated in more detail in order to conclude about transport of water and organic material. We will also investigate the possibility of detection of comets in other planetary systems.

  10. An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

    Wong, Jaslyn E. M. M. [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus (Denmark); Midtgaard, Søren Roi [University of Copenhagen, Universitetsparken 5, 2100 Copenhagen (Denmark); Gysel, Kira [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus (Denmark); Thygesen, Mikkel B.; Sørensen, Kasper K.; Jensen, Knud J. [University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C (Denmark); Stougaard, Jens; Thirup, Søren; Blaise, Mickaël, E-mail: mickael.blaise@cpbs.cnrs.fr [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus (Denmark)

    2015-03-01

    The crystal and solution structures of the T. thermophilus NlpC/P60 d, l-endopeptidase as well as the co-crystal structure of its N-terminal LysM domains bound to chitohexaose allow a proposal to be made regarding how the enzyme recognizes peptidoglycan. LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.

  11. New insights into the dual fluorescence of methyl salicylate: effects of intermolecular hydrogen bonding and solvation.

    Zhou, Panwang; Hoffmann, Mark R; Han, Keli; He, Guozhong

    2015-02-12

    In this paper, we propose a new and complete mechanism for dual fluorescence of methyl salicylate (MS) under different conditions using a combined experimental (i.e., steady-state absorption and emission spectra and time-resolved fluorescence spectra) and theoretical (i.e., time-dependent density function theory) study. First, our theoretical study indicates that the barrier height for excited state intramolecular proton transfer (ESIPT) reaction of ketoB depends on the solvent polarity. In nonpolar solvents, the ESIPT reaction of ketoB is barrierless; the barrier height will increase with increasing solvent polarity. Second, we found that, in alcoholic solvents, intermolecular hydrogen bonding plays a more important role. The ketoB form of MS can form two hydrogen bonds with alcoholic solvents; one will facilitate ESIPT and produce the emission band in the blue region; the other one precludes ESIPT and produces the emission band in the near-UV region. Our proposed new mechanism can well explain previous results as well as our new experimental results.

  12. Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

    Dellerue, Serge

    2000-01-01

    Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr

  13. Chemical origin of blue- and redshifted hydrogen bonds: intramolecular hyperconjugation and its coupling with intermolecular hyperconjugation.

    Li, An Yong

    2007-04-21

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

  14. A molecular dynamics simulation study of chloroform

    Tironi, Ilario G.; van Gunsteren, Wilfred F.

    Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

  15. Dimensionless study on dynamics of pressure controlled mechanical ventilation system

    Shi, Yan; Niu, Jinglong; Cai, Maolin; Xu, Weiqing

    2015-01-01

    Dynamics of mechanical ventilation system can be referred in pulmonary diagnostics and treatments. In this paper, to conveniently grasp the essential characteristics of mechanical ventilation system, a dimensionless model of mechanical ventilation system is presented. For the validation of the mathematical model, a prototype mechanical ventilation system of a lung simulator is proposed. Through the simulation and experimental studies on the dimensionless dynamics of the mechanical ventilation system, firstly, the mathematical model is proved to be authentic and reliable. Secondly, the dimensionless dynamics of the mechanical ventilation system are obtained. Last, the influences of key parameters on the dimensionless dynamics of the mechanical ventilation system are illustrated. The study provides a novel method to study the dynamic of mechanical ventilation system, which can be referred in the respiratory diagnostics and treatment.

  16. Dimensionless study on dynamics of pressure controlled mechanical ventilation system

    Shi, Yan; Niu, Jinglong; Cai, Maolin; Xu, Weiqing [Beihang University, Beijing (Korea, Republic of)

    2015-02-15

    Dynamics of mechanical ventilation system can be referred in pulmonary diagnostics and treatments. In this paper, to conveniently grasp the essential characteristics of mechanical ventilation system, a dimensionless model of mechanical ventilation system is presented. For the validation of the mathematical model, a prototype mechanical ventilation system of a lung simulator is proposed. Through the simulation and experimental studies on the dimensionless dynamics of the mechanical ventilation system, firstly, the mathematical model is proved to be authentic and reliable. Secondly, the dimensionless dynamics of the mechanical ventilation system are obtained. Last, the influences of key parameters on the dimensionless dynamics of the mechanical ventilation system are illustrated. The study provides a novel method to study the dynamic of mechanical ventilation system, which can be referred in the respiratory diagnostics and treatment.

  17. Observing Solvation Dynamics with Simultaneous Femtosecond X-ray Emission Spectroscopy and X-ray Scattering

    Haldrup, Kristoffer; Gawelda, Wojciech; Abela, Rafael

    2016-01-01

    and structural changes, and local solvent structural changes are desired. We have studied the intra- and intermolecular dynamics of a model chromophore, aqueous [Fe(bpy)3]2+, with complementary X-ray tools in a single experiment exploiting intense XFEL radiation as a probe. We monitored the ultrafast structural...... rearrangement of the solute with X-ray emission spectroscopy, thus establishing time zero for the ensuing X-ray diffuse scattering analysis. The simultaneously recorded X-ray diffuse scattering atterns reveal slower subpicosecond dynamics triggered by the intramolecular structural dynamics of the photoexcited...

  18. Model for the dynamic study of AC contactors

    Corcoles, F.; Pedra, J.; Garrido, J.P.; Baza, R. [Dep. d' Eng. Electrica ETSEIB. UPC, Barcelona (Spain)

    2000-08-01

    This paper proposes a model for the dynamic analysis of AC contactors. The calculation algorithm and implementation are discussed. The proposed model can be used to study the influence of the design parameters and the supply in their dynamic behaviour. The high calculation speed of the implemented algorithm allows extensive ranges of parameter variations to be analysed. (orig.)

  19. Towards a Quantum Dynamical Study of the H_2O+H_2O Inelastic Collision: Representation of the Potential and Preliminary Results

    Ndengue, Steve Alexandre; Dawes, Richard

    2017-06-01

    Water, an essential ingredient of life, is prevalent in space and various media. H_2O in the gas phase is the major polyatomic species in the interstellar medium (ISM) and a primary target of current studies of collisional dynamics. In recent years a number of theoretical and experimental studies have been devoted to H_2O-X (with X=He, H_2, D_2, Ar, ?) elastic and inelastic collisions in an effort to understand rotational distributions of H_2O in molecular clouds. Although those studies treated several abundant species, no quantum mechanical calculation has been reported to date for a nonlinear polyatomic collider. We present in this talk the preliminary steps toward this goal, using the H_2O molecule itself as our collider, the very accurate MB-Pol surface to describe the intermolecular interaction and the MultiConfiguration Time Dependent (MCTDH) algorithm to study the dynamics. One main challenge in this effort is the need to express the Potential Energy Surface (PES) in a sum-of-products form optimal for MCTDH calculations. We will describe how this was done and present preliminary results of state-to-state probabilities.

  20. Resolution enhancement in MR spectroscopy of red bone marrow fat via intermolecular double-quantum coherences

    Bao, Jianfeng; Cui, Xiaohong; Huang, Yuqing; Zhong, Jianhui; Chen, Zhong

    2015-08-01

    High-resolution 1H magnetic resonance spectroscopy (MRS) is generally inaccessible in red bone marrow (RBM) tissues using conventional MRS techniques. This is because signal from these tissues suffers from severe inhomogeneity in the main static B0 field originated from the intrinsic honeycomb structures in trabecular bone. One way to reduce effects of B0 field inhomogeneity is by using the intermolecular double quantum coherence (iDQC) technique, which has been shown in other systems to obtain signals insensitive to B0 field inhomogeneity. In the present study, we employed an iDQC approach to enhance the spectral resolution of RBM. The feasibility and performance of this method for achieving high resolution MRS was verified by experiments on phantoms and pig vertebral bone samples. Unsaturated fatty acid peaks which overlap in the conventional MRS were well resolved and identified in the iDQC spectrum. Quantitative comparison of fractions of three types of fatty acids was performed between iDQC spectra on the in situ RMB and conventional MRS on the extracted fat from the same RBM. Observations of unsaturated fatty acids with iDQC MRS may provide valuable information and may hold potential in diagnosis of diseases such as obesity, diabetes, and leukemia.

  1. "Precipitation on Nanoparticles": Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.

    Chu, Zonglin; Han, Yanxiao; Kral, Petr; Klajn, Rafal

    2018-04-19

    Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self-assembled monolayers obtained by co-adsorption from solution of two different molecules. Here, we study co-adsorption of two thiolated ligands-a dialkylviologen and a zwitterionic sulfobetaine-that can interact with each other electrostatically, onto gold nanoparticles. Consequently, the nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. We show that changing the solution molar ratio of two ligands by a factor of ~5,000 affects the on-nanoparticle ratio of these ligands by only 3 times. This behavior is reminiscent of the formation of insoluble inorganic salts (e.g., AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well-defined hybrid organic-inorganic nanostructures. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Intermolecular and very strong intramolecular C-SeO/N chalcogen bonds in nitrophenyl selenocyanate crystals.

    Wang, Hui; Liu, Ju; Wang, Weizhou

    2018-02-14

    Single-crystal X-ray diffraction reveals that polymorphic ortho-nitrophenyl selenocyanate (o-NSC, crystals 1a and 1b) and monomorphic para-nitrophenyl selenocyanate (p-NSC, crystal 2) crystals are all stabilized mainly by intermolecular and very strong intramolecular C-SeO/N chalcogen bonds, as well as by other different interactions. Thermogravimetric (TG) and differential scanning calorimetry thermogram (DSC) analyses show that the starting decomposition temperatures and melting points of the three crystals are different, following the order 1b > 1a > 2, which is consistent with the structural characteristics of the crystals. In addition, atoms in molecules (AIM) and natural bond orbital (NBO) analyses indicate that the total strengths of the C-SeO and C-SeN chalcogen bonds decrease in the order 1b > 1a > 2. This study could be significant for engineering functional crystals based on robust C-SeO and C-SeN chalcogen bonds, and for designing drugs containing selenium as well as understanding their interaction in biosystems.

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

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

    2014-10-01

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

  4. Competition between intermolecular interaction and configuration entropy as the structure-determining factor for inclusion compounds

    Subbotin, O.; Belosludov, V.; Adamova, T. [Russian Academy of Science, Novosibirsk (Russian Federation). Nikolaev Inst. of Inorganic Chemistry; Belosludov, R.; Kawazoe, Y. [Tohoku Univ., Aoba-ku, Sendai (Japan). Inst. for Materials Research; Kudoh, J.I. [Tohoku Univ., Aoba-ku, Sendai (Japan). Center for Northeast Asia Studies

    2008-07-01

    This paper presented a newly developed method to accurately predict the thermodynamic properties of clathrate hydrates, particularly their structural phase transitions under pressure. The method is based on the theory of Van-der-Waals and Platteeuw with some modifications that include the influence of guest molecules on the host lattice. The model was used to explain the exception from the established rule that small guest molecules form structure s1 and large molecules form structure s2 hydrates. In this study, the thermodynamic properties of argon (Ar) hydrate and methane hydrate, each in both cubic structure s1 and s2 were modelled. The model showed that two competing factors play a role in the formation of inclusions, notably the intermolecular interaction of guest molecules with water molecules, and the configuration entropy. Competition of these 2 factors determines the structure of hydrate formed at different pressures. The model provides an accurate description of the thermodynamic properties of gas hydrates and how they behave under pressure. For the argon hydrates, the structural phase transition from structure s2 to s1 at high pressure was predicted, while methane hydrates were predicted to be metastable in the s2 structure. The model can be used for other inclusion compounds with the same type of composition such as clathrate silicon, zeolites, and inclusion compounds of semiconductor elements. 17 refs., 5 figs.

  5. Intermolecular interaction potentials of the methane dimer from the local density approximation

    Chen Xiangrong; Bai Yulin; Zhu Jun; Yang Xiangdong

    2004-01-01

    The intermolecular interaction potentials of methane (CH 4 ) dimer are calculated within the density functional theory in the local density approximation (LDA). It is found that the calculated potentials have minima when the intermolecular distance of CH 4 dimer is about 7.0 a.u., which is in good agreement with the experiment. The depth of the potential is 0.017 eV. The results obtained by our LDA calculations seem to agree well with those obtained by MP2, MP3, and CCSD from the Moeller-Plesset and coupled cluster methods by Tsuzuki et al. and with the experimental data

  6. Dynamical study of symmetries: breaking and restauration

    Schuck, P.

    1986-09-01

    First symmetry breaking (spontaneous) is explained and the physical implication discussed for infinite systems. The relation with phase transitions is indicated. Then the specific aspects of symmetry breaking in finite systems is treated and illustrated in detail for the case of translational invariance with the help of an oversimplified but exactly solvable model. The method of projection (restauration of symmetry) is explained for the static case and also applied to the model. Symmetry breaking in the dynamical case and for instance the notion of a soft mode responsible for the symmetry breaking is discussed in the case of superfluidity and another exactly solvable model is introduced. The Goldstone mode is treated in detail. Some remarks on analogies with the breaking of chiral symmetry are made. Some recent developments in the theory of symmetry restauration are briefly outlined [fr

  7. Systems approaches to study root architecture dynamics

    Candela eCuesta

    2013-12-01

    Full Text Available The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation.Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how lateral roots and thereby root system architecture is established and developed.

  8. Study of a spur gear dynamic behavior in transient regime

    Khabou, M. T.; Bouchaala, N.; Chaari, F.; Fakhfakh, T.; Haddar, M.

    2011-11-01

    In this paper the dynamic behavior of a single stage spur gear reducer in transient regime is studied. Dynamic response of the single stage spur gear reducer is investigated at different rotating velocities. First, gear excitation is induced by the motor torque and load variation in addition to the fluctuation of meshing stiffness due to the variation of input rotational speed. Then, the dynamic response is computed using the Newmark method. After that, a parameter study is made on spur gear powered in the first place by an electric motor and in the second place by four strokes four cylinders diesel engine. Dynamic responses come to confirm a significant influence of the transient regime on the dynamic behavior of a gear set, particularly in the case of engine acyclism condition.

  9. Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

    Yu H. G.; Muckerman, J.T.

    2012-05-29

    The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

  10. Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

    Yu, H.G.; Muckerman, J.T.

    2010-06-01

    The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

  11. Identification of Phytochemicals Targeting c-Met Kinase Domain using Consensus Docking and Molecular Dynamics Simulation Studies.

    Aliebrahimi, Shima; Montasser Kouhsari, Shideh; Ostad, Seyed Nasser; Arab, Seyed Shahriar; Karami, Leila

    2018-06-01

    c-Met receptor tyrosine kinase is a proto-oncogene whose aberrant activation is attributed to a lower rate of survival in most cancers. Natural product-derived inhibitors known as "fourth generation inhibitors" constitute more than 60% of anticancer drugs. Furthermore, consensus docking approach has recently been introduced to augment docking accuracy and reduce false positives during a virtual screening. In order to obtain novel small-molecule Met inhibitors, consensus docking approach was performed using Autodock Vina and Autodock 4.2 to virtual screen Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database against active and inactive conformation of c-Met kinase domain structure. Two hit molecules that were in line with drug-likeness criteria, desired docking score, and binding pose were subjected to molecular dynamics simulations to elucidate intermolecular contacts in protein-ligand complexes. Analysis of molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area studies showed that ZINC08234189 is a plausible inhibitor for the active state of c-Met, whereas ZINC03871891 may be more effective toward active c-Met kinase domain compared to the inactive form due to higher binding energy. Our analysis showed that both the hit molecules formed hydrogen bonds with key residues of the hinge region (P1158, M1160) in the active form, which is a hallmark of kinase domain inhibitors. Considering the pivotal role of HGF/c-Met signaling in carcinogenesis, our results propose ZINC08234189 and ZINC03871891 as the therapeutic options to surmount Met-dependent cancers.

  12. Molecular dynamics studies of displacement cascades

    Averback, R.S.; Hsieh, Horngming; Diaz de la Rubia, T.

    1990-02-01

    Molecular-dynamics simulations of cascades in Cu and Ni with primary-knock-on energies up to 5 keV and lattice temperatures in the range 0 K--700 K are described. Interatomic forces were represented by either the Gibson II (Cu) or Johnson-Erginsoy (Ni) potentials in most of this work, although some simulations using ''Embedded Atom Method'' potentials, e.g., for threshold events in Ni 3 Al, are also presented. The results indicate that the primary state of damage produced by displacement cascades is controlled by two phenomena, replacement collision sequences during the collisional phase of the cascade and local melting during the thermal spike. As expected, the collisional phase is rather similar in Cu and Ni, however, the thermal spike is of longer duration and has a more pronounced influence in Cu than Ni. When the ambient temperature of the lattice is increased, the melt zones are observed to both increase in size and cool more slowly. This has the effect of reducing defect production and enhancing atomic mixing and disordering. The implications of these results for defect production, cascade collapse, atomic disordering will be discussed. 34 refs., 7 figs., 2 tabs

  13. Effect of intermolecular cohesion on coal liquefaction. 3. Reactivity of oxygen methylated coal; Sekitan teibunshika hanno ni okeru bunshikan gyoshuryoku no koka. 3. O-methyl ka tan no hanno tokusei

    Sasaki, M.; Nagaishi, H.; Yoshida, T. [Hokkaido National Industrial Research Institute, Sapporo (Japan)

    1996-10-28

    The reactivity of oxygen methylated coal was studied to control hydrogen bond in bituminous coal liquefaction and intermolecular cohesion such as van der Waals force. In experiment, crushed and dried Illinois coal of 100mesh or less was used as specimen, and oxygen methylated coal was prepared by Liotta`s method using tetrabutylammonium halide. Coal liquefaction was conducted in an electromagnetic agitation autoclave using tetralin solvent under initial hydrogen pressure of 100kg/cm{sup 2} while heating. The molecular weight distribution of the products obtained was measured by gel permeation chromatography (GPC) analysis. The experimental results are as follows. The effect of intermolecular cohesion in bituminous coal on the reactivity is mainly derived from decomposing reaction from preasphaltene to oil. Yields of oil fraction by methylation increase corresponding to release of intermolecular cohesion. Since the thermal release is promoted with temperature rise, the difference in yield due to different treatments decreases. 5 refs., 3 figs., 1 tab.

  14. Dynamical study of a polydisperse hard-sphere system

    Nogawa, Tomoaki; Ito, Nobuyasu; Watanabe, Hiroshi

    2010-01-01

    We study the interplay between the fluid-crystal transition and the glass transition of elastic sphere system with polydispersity using nonequilibrium molecular dynamics simulations. It is found that the end point of the crystal-fluid transition

  15. Concentration dynamics in lakes and reservoirs. Studies using radioactive tracers

    Gilath, Ch.

    1983-01-01

    The use of radioactive tracers for the investigation of concentration dynamics of inert soluble matter in lakes and reservoirs is reviewed. Shallow and deep stratified lakes are considered. The mechanism of mixing in lakes, flow pattern and input - output response are discussed. The methodology of the use of radioactive tracers for concentration dynamic studies is described. Examples of various investigations are reviewed. The dynamics of shallow lakes can be found and expressed in terms of transfer functions, axial dispersion models, residence time distributions and sometimes only semiquantitative information about the flow pattern. The dynamics of deep, stratified lakes is more complex and difficult to investigate with tracers. Flow pattern, horizontal and vertical eddy diffusivities, mass transfer between the hypolimnion and epilimnion are tools used for describing this dynamics. (author)

  16. Study on dynamic lifting characteristics of control rod drive mechanism

    Shen Xiaoyao

    2012-01-01

    Based on the equations of the electric circuit and the magnetic circuit and analysis of the dynamic lifting process for the control rod drive mechanism (CRDM), coupled magnetic-electric-mechanical equations both for the static status and the dynamic status are derived. The analytical method is utilized to obtain the current and the time when the lift starts. The numerical simulation method of dynamic analysis recommended by ASME Code is utilized to simulate the dynamic lifting process of CRDM, and the dynamic features of the system with different design gaps are studied. Conclusions are drawn as: (1) the lifting-start time increases with the design gap, and the time for the lifting process is longer with larger gaps; (2) the lifting velocity increases with time; (3) the lifting acceleration increases with time, and with smaller gaps, the impact acceleration is larger. (author)

  17. Instability and dynamics of volatile thin films

    Ji, Hangjie; Witelski, Thomas P.

    2018-02-01

    Volatile viscous fluids on partially wetting solid substrates can exhibit interesting interfacial instabilities and pattern formation. We study the dynamics of vapor condensation and fluid evaporation governed by a one-sided model in a low-Reynolds-number lubrication approximation incorporating surface tension, intermolecular effects, and evaporative fluxes. Parameter ranges for evaporation-dominated and condensation-dominated regimes and a critical case are identified. Interfacial instabilities driven by the competition between the disjoining pressure and evaporative effects are studied via linear stability analysis. Transient pattern formation in nearly flat evolving films in the critical case is investigated. In the weak evaporation limit unstable modes of finite-amplitude nonuniform steady states lead to rich droplet dynamics, including flattening, symmetry breaking, and droplet merging. Numerical simulations show that long-time behaviors leading to evaporation or condensation are sensitive to transitions between filmwise and dropwise dynamics.

  18. Decomposition of Intermolecular Interactions in the Crystal Structure of Some Diacetyl Platinum(II Complexes: Combined Hirshfeld, AIM, and NBO Analyses

    Saied M. Soliman

    2016-12-01

    Full Text Available Intermolecular interactions play a vital role in crystal structures. Therefore, we conducted a topological study, using Hirshfeld surfaces and atom in molecules (AIM analysis, to decompose and analyze, respectively, the different intermolecular interactions in six hydrazone-diacetyl platinum(II complexes. Using AIM and natural bond orbital (NBO analyses, we determined the type, nature, and strength of the interactions. All the studied complexes contain C-H⋯O interactions, and the presence of bond critical points along the intermolecular paths underlines their significance. The electron densities (ρ(r at the bond critical points (0.0031–0.0156 e/a03 fall within the typical range for H-bonding interactions. Also, the positive values of the Laplacian of the electron density (∇2ρ(r revealed the depletion of electronic charge on the interatomic path, another characteristic feature of closed-shell interactions. The ratios of the absolute potential energy density to the kinetic energy density (|V(r|/G(r and ρ(r are highest for the O2⋯H15-N3 interaction in [Pt(COMe2(2-pyCMe=NNH2] (1; hence, this interaction has the highest covalent character of all the O⋯H intermolecular interactions. Interestingly, in [Pt(COMe2(H2NN=CMe-CMe=NNH2] (3, there are significant N-H⋯Pt interactions. Using the NBO method, the second-order interaction energies, E(2, of these interactions range from 3.894 to 4.061 kJ/mol. Furthermore, the hybrid Pt orbitals involved in these interactions are comprised of dxy, dxz, and s atomic orbitals.

  19. Catalytic Intermolecular Cross-Couplings of Azides and LUMO-Activated Unsaturated Acyl Azoliums

    Li, Wenjun

    2017-02-15

    An example for the catalytic synthesis of densely functionalized 1,2,3-triazoles through a LUMO activation mode has been developed. The protocol is enabled by intermolecular cross coupling reactions of azides with in situ-generated alpha,beta-unsaturated acyl azoliums. High yields and broad scope as well as the investigation of reaction mechanism are reported.

  20. Ab initio and Gordon--Kim intermolecular potentials for two nitrogen molecules

    Ree, F.H.; Winter, N.W.

    1980-01-01

    Both ab initio MO--LCAO--SCF and the electron-gas (or Gordon--Kim) methods have been used to compute the intermolecular potential (Phi) of N 2 molecules for seven different N 2 --N 2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for Phi>0.002 hartree or intermolecular separations less than 6.5--7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N 2 molecules. The Gordon--Kim method with Rae's self-exchange correction yields Phi, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon--Kim calculations. Using the ab initio data we derive an atom--atom potential of the two N 2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio Phi remarkably well. The spherically averaged ab initio Phi is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio Phi to the classical quadrupole--quadrupole interaction at large intermolecular separation is also discussed

  1. Strong Intermolecular Exciton Couplings in Solid-State Circular Dichroism of Aryl Benzyl Sulfoxides

    Padula, Daniele; Di Pietro, S.; Capozzi, M. A. M.; Cardellicchio, C.; Pescitelli, G.

    2014-01-01

    Roč. 26, č. 9 (2014), s. 462-470 ISSN 0899-0042 Institutional support: RVO:61388963 Keywords : organic crystals * TDDFT CD calculations * pairwise additive approximation * two-body effects * intermolecular forces in crystal lattices Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.886, year: 2014

  2. Salting Effects as an Illustration of the Relative Strength of Intermolecular Forces

    Person, Eric C.; Golden, Donnie R.; Royce, Brenda R.

    2010-01-01

    This quick and inexpensive demonstration of the salting of an alcohol out of an aqueous solution illustrates the impact of intermolecular forces on solubility using materials familiar to many students. Ammonium sulfate (fertilizer) is added to an aqueous 35% solution of isopropyl alcohol (rubbing alcohol and water) containing food coloring as a…

  3. An Analytical Study of Prostate-Specific Antigen Dynamics.

    Esteban, Ernesto P; Deliz, Giovanni; Rivera-Rodriguez, Jaileen; Laureano, Stephanie M

    2016-01-01

    The purpose of this research is to carry out a quantitative study of prostate-specific antigen dynamics for patients with prostatic diseases, such as benign prostatic hyperplasia (BPH) and localized prostate cancer (LPC). The proposed PSA mathematical model was implemented using clinical data of 218 Japanese patients with histological proven BPH and 147 Japanese patients with LPC (stages T2a and T2b). For prostatic diseases (BPH and LPC) a nonlinear equation was obtained and solved in a close form to predict PSA progression with patients' age. The general solution describes PSA dynamics for patients with both diseases LPC and BPH. Particular solutions allow studying PSA dynamics for patients with BPH or LPC. Analytical solutions have been obtained and solved in a close form to develop nomograms for a better understanding of PSA dynamics in patients with BPH and LPC. This study may be useful to improve the diagnostic and prognosis of prostatic diseases.

  4. Backtracing neutron analysis in the fusion-fission dynamics study

    Brennand, E. de Goes; Hanappe, F.; Stuttge, L.

    2001-01-01

    A new method for the analysis of multi parametric experimental data is used in the study of the dynamics of the fission process for the compound system 126 Ba. We apply this method to obtain the correlation between thermal energy related to the neutron total multiplicity and the correlation between pre-scission neutron and pos-scission neutron multiplicities. The results obtained are interpreted into the framework of a dynamical model. From this interpretation we have access to the following information: the friction intensity which drives the dynamical evolution of the system; the initial deformation of the compound system; the barrier evolution with temperature and angular momentum, and fission times. (author)

  5. Temperature dependent dynamics of DegP-trimer: A molecular dynamics study

    Nivedita Rai

    2015-01-01

    Full Text Available DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46–80 of LA loop express a flip towards right (at 280 and left ( at 320 K with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

  6. NASA plan for international crustal dynamics studies

    1979-01-01

    The international activities being planned as part of the NASA geodynamics program are described. Methods of studying the Earth's crustal movements and deformation characteristics are discussed. The significance of the eventual formalations of earthquake predictions methods is also discussed.

  7. Effects of intermolecular interactions on the stability of carbon nanotube–gold nanoparticle conjugates in solution

    Konczak L

    2016-11-01

    Full Text Available Lukasz Konczak,1 Jolanta Narkiewicz-Michalek,2 Giorgia Pastorin,3 Tomasz Panczyk1 1Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Cracow, 2Department of Chemistry, Maria Curie-Sklodowska University, Lublin, Poland; 3Department of Pharmacy, National University of Singapore, Singapore Abstract: This work deals with the role of intermolecular interactions in the stability of a carbon nanotube (CNT capped by functionalized gold nanoparticles (AuNPs. The importance of such a system is due to its potential application as a pH-controlled drug carrier. Our preliminary experimental studies showed that fabrication of such a nanobottle/nanocontainer is feasible and it is possible to encapsulate the anticancer drug cisplatin inside the inner space of a CNT and seal its ends by functionalized AuNPs. The expected behavior, that is, detachment of AuNPs at acidic pH and the release of cisplatin, was, however, not observed. On the other hand, our theoretical studies of chemically identical system led to the conclusion that the release of cisplatin at acidic pH should be observed. Therefore, in this work, a deeper theoretical analysis of various factors that could be responsible for the disagreement between experimental and theoretical results were performed. The study found that the major factor is a large dispersion interaction component acting between CNT and AuNP in solution in the case of the experimental system. This factor can be controlled to some extent by tuning the system size or the ratio between AuNP diameter and CNT diameter. Thus, such kind of a pH-sensitive drug carrier is still of great interest, but its structural parameters need to be properly adjusted. Keywords: hydrazone bond, drug delivery, dispersion interactions, cisplatin, acidic pH

  8. Effects of intermolecular interactions on absorption intensities of the fundamental and the first, second, and third overtones of OH stretching vibrations of methanol and t-butanol‑d9 in n-hexane studied by visible/near-infrared/infrared spectroscopy

    Morisawa, Yusuke; Suga, Arisa

    2018-05-01

    Visible (Vis), near-infrared (NIR) and IR spectra in the 15,600-2500 cm- 1 region were measured for methanol, methanol-d3, and t-butanol-d9 in n-hexane to investigate effects of intermolecular interaction on absorption intensities of the fundamental and the first, second, and third overtones of their OH stretching vibrations. The relative area intensities of OH stretching bands of free and hydrogen-bonded species were plotted versus the vibrational quantum number using logarithm plots (V = 1-4) for 0.5 M methanol, 0.5 M methanol‑d3, and 0.5 M t-butanol-d9 in n-hexane. In the logarithm plots the relative intensities of free species yield a linear dependence irrespective of the solutes while those of hydrogen-bonded species deviate significantly from the linearity. The observed results suggest that the modifications in dipole moment functions of the OH bond induced by the formation of the hydrogen bondings change transient dipole moment, leading to the deviations of the dependences of relative absorption intensities on the vibrational quantum number from the linearity.

  9. Study on Human-structure Dynamic Interaction in Civil Engineering

    Gao, Feng; Cao, Li Lin; Li, Xing Hua

    2018-06-01

    The research of human-structure dynamic interaction are reviewed. Firstly, the influence of the crowd load on structural dynamic characteristics is introduced and the advantages and disadvantages of different crowd load models are analyzed. Then, discussing the influence of structural vibration on the human-induced load, especially the influence of different stiffness structures on the crowd load. Finally, questions about human-structure interaction that require further study are presented.

  10. Dynamic scintigraphic studies after oesophageal reconstruction

    Maliska, C.M.; Maliska, C.; Pinto, E.; Castro, L.; Fonseca, L.B.E; Miranda, M.

    1997-01-01

    Full text: We have studied the oesophageal transit and gastric emptying in the monitoring of the effect of oesophageal reconstruction surgery. Oncologic patients were evaluated after oesophageal reconstruction surgery with gastric (14 patients) or colonic (5 patients) tube and they were compared with 15 healthy volunteers, using scintigraphic method with liquid food (S-colloid-Tc99m). In the oesophageal transit studies there were no significant statistical differences among the three groups, when we have just considered to two superior (of the three) segments, as oesophagus, showing that the distal neo-tube works just like the stomach of normal volunteers

  11. Probing Intermolecular Electron Delocalization in Dimer Radical Anions by Vibrational Spectroscopy

    Mani, Tomoyasu; Brookhaven National Laboratory; Grills, David C.

    2017-01-01

    Delocalization of charges is one of the factors controlling charge transport in conjugated molecules. It is considered to play an important role in the performance of a wide range of molecular technologies, including organic solar cells and organic electronics. Dimerization reactions are well-suited as a model to investigate intermolecular spatial delocalization of charges. And while dimerization reactions of radical cations are well investigated, studies on radical anions are still scarce. Upon dimerization of radical anions with neutral counterparts, an electron is considered to delocalize over the two molecules. By using time-resolved infrared (TRIR) detection coupled with pulse radiolysis, we show that radical anions of 4-n-hexyl-4'-cyanobiphenyl (6CB) undergo such dimerization reactions, with an electron equally delocalized over the two molecules. We have recently demonstrated that nitrile ν(C≡N) vibrations respond to the degree of electron localization of nitrile-substituted anions: we can quantify the changes in the electronic charges from the neutral to the anion states in the nitriles by monitoring the ν(C≡N) IR shifts. In the first part of this article, we show that the sensitivity of the ν(C≡N) IR shifts does not depend on solvent polarity. In the second part, we describe how probing the shifts of the nitrile IR vibrational band unambiguously confirms the formation of dimer radical anions, with K dim = 3 × 10 4 M –1 . IR findings are corroborated by electronic absorption spectroscopy and electronic structure calculations. We find that the presence of a hexyl chain and the formation of π–π interactions are both crucial for dimerization of radical anions of 6CB with neutral 6CB. Our study provides clear evidence of spatial delocalization of electrons over two molecular fragments.

  12. Fundamental study of dynamic ECT by dual detector gammacamera system

    Kakegawa, M.; Matsui, S.; Maeda, H.; Takeda, K.; Nakagawa, T.

    1982-01-01

    The improvement of image quality of reconstructed image by the simple pre-processing of projections is studied. Using the improved algorithm and dual detector gammacamera system, the possibility of dynamic ECT is studied. As shown in clinical examples, renal flow study using Tc-99m-DTPA, dynamic ECT imaging is possible with measuring time of 1 or 2 minutes. By this method cortex and medulla are separately imaged and each function can be analyzed more precisely. Using high sensitive collimator it will be possible to take ECT images every 30 sec. with little resolution loss quantitative three dimensional time activity analysis is under study

  13. Clinical application of cerebral dynamic perfusion studies

    DeLand, F.H.

    1975-01-01

    Radionuclide cerebral perfusion studies are assuming a far greater importance in the detection and differential diagnosis of cerebral lesions. Perfusion studies not only contribute to the differential diagnosis of lesions but in certain cases are the preferred methods by which more accurate clinical interpretations can be made. The characteristic blood flow of arterio-venous malformations readily differentiates this lesion from neoplasms. The decreased perfusion or absent perfusion observed in cerebral infarctions is diagnostic without concurrent evidence from static images. Changes in rates and direction of blood flow contribute fundamental information to the status of stenosis and vascular occlusion and, in addition, offer valuable information on the competency and routes of collateral circulation. The degree of cerebral perfusion after cerebral vascular accidents appears to be directly related to patient recovery, particularly muscular function. Cerebral perfusion adds a new parameter in the diagnosis of subdural haematomas and concussion and in the differentiation of obscuring radioactivity from superficial trauma. Although pictorial displays of perfusion blood flow will offer information in most cerebral vascular problems, the addition of computer analysis better defines temporal relationships of regional blood flow, quantitative changes in flow and the detection of the more subtle increases or decreases in cerebral blood flow. The status of radionuclide cerebral perfusion studies has taken on an importance making it the primary modality for the diagnosis of cerebral lesions. (author)

  14. NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics

    Capellos, Christos

    1986-01-01

    This book contains the formal lectures and contributed papers presented at the NATO Advanced Study Institute on. the Advances in Chemical Reaction Dynamics. The meeting convened at the city of Iraklion, Crete, Greece on 25 August 1985 and continued to 7 September 1985. The material presented describes the fundamental and recent advances in experimental and theoretical aspects of, reaction dynamics. A large section is devoted to electronically excited states, ionic species, and free radicals, relevant to chemical sys­ tems. In addition recent advances in gas phase polymerization, formation of clusters, and energy release processes in energetic materials were presented. Selected papers deal with topics such as the dynamics of electric field effects in low polar solutions, high electric field perturbations and relaxation of dipole equilibria, correlation in picosecond/laser pulse scattering, and applications to fast reaction dynamics. Picosecond transient Raman spectroscopy which has been used for the elucidati...

  15. Microscopic study on dynamic barrier in fusion reactions

    Wu Xizhen; Tian Junlong; Zhao Kai; Li Zhuxia; Wang Ning

    2004-01-01

    The authors briefly review the fusion process of very heavy nuclear systems and some theoretical models. The authors propose a microscopic transport dynamic model, i.e. the Improved Quantum Molecular Dynamic model, for describing fusion reactions of heavy systems, in which the dynamical behavior of the fusion barrier in heavy fusion systems has been studied firstly. The authors find that with the incident energy decreasing the lowest dynamic barrier is obtained which approaches to the adiabatic static barrier and with increase of the incident energy the dynamic barrier goes up to the diabatic static barrier. The authors also indicate that how the dynamical fusion barrier is correlated with the development of the configuration of fusion partners along the fusion path. Associating the single-particle potentials obtained at different stages of fusion with the Two Center Shell Model, authors can study the time evolution of the single particle states of fusion system in configuration space of single particle orbits along the fusion path. (author)

  16. Studies of Beam Dynamics in Cooler Rings

    Dietrich, J.; Stein, J.; Meshkov, I.; Sidorin, A.; Smirnov, A.

    2006-01-01

    This report describes the numerical simulation of the crystalline proton beam formation in COSY using BETACOOL code. The study includes the description of experimental results at NAP-M storage ring where the large reduction of the momentum spread was observed for first time. The present simulation shows that this behavior of proton beam can not be explained as ordered state of protons. The numerical simulation of crystalline proton beams was done for COSY parameters. The number of protons when the ordering state can be observed is limited by value 106 particles and momentum spread less then 10-6. Experimental results for the attempt to achieve of ordered state of proton beam for COSY is presented. This work is supported by RFBR grant no. 05-02-16320 and INTAS grant no. 03-54-5584

  17. RF quadrupole beam dynamics design studies

    Crandall, K.R.; Stokes, R.H.; Wangler, T.P.

    1979-01-01

    The radio-frequency quadrupole (RFQ) linear accelerator structure is expected to permit considerable flexibility in achieving linac design objectives at low velocities. Calculational studies show that the RFQ can accept a high-current, low-velocity, dc beam, bunch it with high efficiency, and accelerate it to a velocity suitable for injection into a drift-tube linac. Although it is relatively easy to generate a satisfactory design for an RFQ linac for low beam currents, the space-charge effects produced by high currents dominate the design criteria. Methods have been developed to generate solutions that make suitable compromises between the effects of emittance growth, transmission efficiency, and overall structure length. Results are given for a test RFQ linac operating at 425 MHz

  18. Structural, dynamical, and electronic properties of amorphous silicon: An ab initio molecular dynamics study

    Car, R.; Parrinello, M.

    1988-01-18

    An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.

  19. Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

    De Leeuw, S.W.; Brakkee, M.J.D.

    1990-01-01

    Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

  20. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

  1. STUDY ON HEAT DYNAMIC LOADING OF RUBBER

    T. I. Igumenova

    2015-01-01

    Full Text Available A number of studies on heat buildup in tire rubber surface scan method samples using a thermal imaging camera. Investigated the exothermic chemical reaction mechanical destruction rubber when loading designs permanent cyclic stretching with deformation of the working zone 50%. Percentage of deformation of the working zone was chosen on the basis of the actual data on the stretch-compression zone "Rusk" tires, which is the maximum level difference of deformation during run-in. Experiment plan provided for periodic relaxation samples of at least 72 hours for more accurate simulation of operation process of structural products. Created and processed data on temperature changes in samples for bar and line profile for rubber compounds with the introduction of nanomodifiers (fulleren technical carbon in comparison with the control sample without him. The data obtained reflect the nature of heat depending on the composition of the compound. Identified common patterns of thermal nature of physico-chemical process mechanical destruction rubbers. For rubber with nanomodifikatorom there has been an increase in the temperature interval reaction from a minimum to a maximum 2 degrees that is also linked to the rise in the average temperature of the reaction on the histogram also at 2-3 degrees of deformation under the same conditions and the level of cyclic loading. However, the temperature in the control sample that is associated with the beginning of the formation of hardened rubber structures, economies of Mallinz-Petrikeev, occurs with delay twice compared with modified Fullerenes. Measurement of physic-mechanical indicators selected in the course of testing of samples showed the beginning of formation of structure with increased strength of samples in the sample temperature zone that corresponds to the thermal effect of èndotermičeskomu recombination reactions of macromolecules.

  2. Studies of Fundamental Particle Dynamics in Microgravity

    Rangel, Roger; Trolinger, James D.; Coimbra, Carlos F. M.; Witherow, William; Rogers, Jan; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    This work summarizes theoretical and experimental concepts used to design the flight experiment mission for SHIVA - Spaceflight Holography Investigation in a Virtual Apparatus. SHIVA is a NASA project that exploits a unique, holography-based, diagnostics tool to understand the behavior of small particles subjected to transient accelerations. The flight experiments are designed for testing model equations, measuring g, g-jitter, and other microgravity phenomena. Data collection will also include experiments lying outside of the realm of existing theory. The regime under scrutiny is the low Reynolds number, Stokes regime or creeping flow, which covers particles and bubbles moving at very low velocity. The equations describing this important regime have been under development and investigation for over 100 years and yet a complete analytical solution of the general equation had remained elusive yielding only approximations and numerical solutions. In the course of the ongoing NASA NRA, the first analytical solution of the general equation was produced by members of the investigator team using the mathematics of fractional derivatives. This opened the way to an even more insightful and important investigation of the phenomena in microgravity. Recent results include interacting particles, particle-wall interactions, bubbles, and Reynolds numbers larger than unity. The Space Station provides an ideal environment for SHIVA. Limited ground experiments have already confirmed some aspects of the theory. In general the space environment is required for the overall experiment, especially for cases containing very heavy particles, very light particles, bubbles, collections of particles and for characterization of the space environment and its effect on particle experiments. Lightweight particles and bubbles typically rise too fast in a gravitational field and heavy particles sink too fast. In a microgravity environment, heavy and light particles can be studied side-by-side for

  3. Central-field intermolecular potentials from the differential elastic scattering of H2(D2) by other molecules

    Kuppermann, Aron; Gordon, R.J.; Coggiola, M.J.

    1974-01-01

    Differential elastic scattering cross sections for the systems H 2 +O 2 , SF 6 , NH 3 , CO, and CH 4 and for D 2 +O 2 , SF 6 , and NH 3 have been obtained from crossed beam studies. In all cases, rapid quantum oscillations have been resolved which permit the determination of intermolecular potentiel parameters if a central-field assumption is adopted. These potentials were found to be independent of both the isotopic form of the hydrogen molecule, and the relative collision energy. As a result of this, and the ability of these spherical potentials to quantitatively describe the measured scattering, it is concluded that anisotropy effects do not seem important in these H 2 (D 2 ) systems

  4. Symmetric bi-pyridyl banana-shaped molecule and its intermolecular hydrogen bonding liquid-crystalline complexes

    Sui, Dan; Hou, Qiufei; Chai, Jia; Ye, Ling; Zhao, Liyan; Li, Min; Jiang, Shimei

    2008-11-01

    A new symmetric bi-pyridyl banana-shaped molecule 1,3-phenylene diisonicotinate (PDI) was designed and synthesized. Its molecular structure was confirmed by FTIR, Elemental analysis and 1H NMR. X-ray crystallographic study reveals that there is an angle of approximate 118° among the centroids of the three rings (pyridyl-phenyl-pyridyl) in each PDI molecule indicating a desired banana shape. In addition, a series of liquid crystal complexes nBA:PDI:nBA induced by intermolecular hydrogen bonding between PDI (proton acceptor) and 4-alkoxybenzoic acids (nBA, proton donor) were synthesized and characterized. The mesomorphism properties and optical textures of the complex of nBA:PDI:nBA were investigated by differential scanning calorimetry, polarizing optical microscope and X-ray diffraction.

  5. Propagator formalism and computer simulation of restricted diffusion behaviors of inter-molecular multiple-quantum coherences

    Cai Congbo; Chen Zhong; Cai Shuhui; Zhong Jianhui

    2005-01-01

    In this paper, behaviors of single-quantum coherences and inter-molecular multiple-quantum coherences under restricted diffusion in nuclear magnetic resonance experiments were investigated. The propagator formalism based on the loss of spin phase memory during random motion was applied to describe the diffusion-induced signal attenuation. The exact expression of the signal attenuation under the short gradient pulse approximation for restricted diffusion between two parallel plates was obtained using this propagator method. For long gradient pulses, a modified formalism was proposed. The simulated signal attenuation under the effects of gradient pulses of different width based on the Monte Carlo method agrees with the theoretical predictions. The propagator formalism and computer simulation can provide convenient, intuitive and precise methods for the study of the diffusion behaviors

  6. Photochemistry of Nitrophenol Molecules and Clusters: Intra- vs Intermolecular Hydrogen Bond Dynamics

    Grygoryeva, Kateřina; Kubečka, J.; Pysanenko, Andriy; Lengyel, Jozef; Slavíček, Petr; Fárník, Michal

    2016-01-01

    Roč. 120, č. 24 (2016), s. 4139-4146 ISSN 1089-5639 R&D Projects: GA ČR(CZ) GA15-12386S Institutional support: RVO:61388955 Keywords : photochemistry * clusters * laser techniques Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.847, year: 2016

  7. Application of single photon ECT for dynamic study

    Mukai, T.; Ishii, Y.; Tamaki, N.

    1982-01-01

    Feasibility of dynamic study in a form of ECT using a rotating gamma camera was evaluated. Since it takes longer one around time sampling, application for the dynamic study is limited under following conditions; 1) physiological gated process, 2) slow clearance process, 3) physiological steady state process. The gated study was applicated for heart pumping action synchronized with ECG. The ECG gated heart ECT either of blood pool or myocardium was useful to reveal a subtle wall motion abnormalities in a tomographic plane, even when a planar imaging failed to reveal it. As for slow dynamic process of tracer, an excretion process of hepatobiliary agent, was subjected to be analyzed in order to calculate clearance rate at each pixel. As for steady state process, an ECT of regional celebral blood flow (rCBF) was investigated during continuous infusion into intracarotid artery. All of these technique were proved to have a clinical feasibility and to potentiate usefulness of the single photon ECT (SPECT)

  8. Study of beam dynamics at cooler synchrotron TARN-II

    Watanabe, S.; Katayama, T.; Watanabe, T.; Yoshizawa, M.; Tomizawa, M.; Chida, K.; Arakaki, Y.; Noda, K.; Kanazawa, M.

    1992-08-01

    Several kinds of beam diagnostic instruments, have been developed at cooler-synchrotron TARN-II. These are intended to study beam dynamics at low beam current of several microamperes and then have high sensitivity of good S/N ratio. In addition, the acceleration system, especially low level RF system, has been improved to attain the maximum beam energy. With the successful performance of these instrumentations, the study of beam dynamics are presently being carried out. For example, the synchrotron acceleration of the light ions was achieved up to 220 MeV/u without any beam loss. (author)

  9. Study of dynamics of level of physical preparedness of students.

    Коvalenko Y.A.

    2010-12-01

    Full Text Available The dynamics of level of physical preparedness of students is studied in the article. A tendency is marked to the decline of level of physical preparedness of students of 1-3 courses. Methodical recommendations are presented on the improvement of the system of organization of physical education of students of the Zaporizhzhya national university. The dynamics of indexes of physical preparedness of students 1, 2, 3 courses of different years of teaching is studied. Principal reasons of decline of level of physical preparedness of students are certain. There are recommendations the department of physical education in relation to physical preparedness of students.

  10. Intermolecular interactions between B. mori silk fibroin and poly(L-lactic acid) in electrospun composite nanofibrous scaffolds

    Taddei, Paola, E-mail: paola.taddei@unibo.it [Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna (Italy); Tozzi, Silvia [Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna (Italy); Zuccheri, Giampaolo [Dipartimento di Farmacia e Biotecnologie e Centro Interdipartimentale di Ricerca Industriale Scienze della Vita e Tecnologie per la Salute, Università di Bologna, Via Irnerio 48, 40126 Bologna (Italy); Centro S3, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (Italy); Martinotti, Simona; Ranzato, Elia [Dipartimento di Scienze e Innovazione Tecnologica, DiSIT, Università del Piemonte Orientale, viale Teresa Michel 11, 15121 Alessandria (Italy); Chiono, Valeria; Carmagnola, Irene [Dipartimento di Ingegneria Meccanica e Aerospaziale, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Tsukada, Masuhiro [Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567 (Japan)

    2017-01-01

    In this study, composite nanofibrous scaffolds were obtained by electrospinning a trifluoroacetic acid solution containing B. mori silk fibroin (SF) and poly(L-lactic acid) (PLLA) in a 1:1 weight ratio. SF, PLLA and SF/PLLA nanofibres were prepared with average diameter sizes of 360 ± 90 nm, 470 ± 240 nm and 580 ± 220 nm, respectively, as assessed by SEM analysis. Vibrational and thermal analyses showed that upon blending in the SF/PLLA nanofibres, the crystallisation of PLLA was hindered by the presence of SF, which crystallized preferentially and underwent conformational changes that did not significantly change its prevailing β-sheet structure. The two components were thermodynamically compatible and the intermolecular interactions between them were revealed for the first time. Human keratinocytes were cultured on nanofibres and their viability and proliferation were determined. Preliminary in vitro tests showed that the incorporation of SF into the PLLA component enhanced cell adhesion and proliferation with respect to the unfunctionalised material. SF has been successfully used to modify the biomaterial properties and confirmed to be an efficient bioactive protein to mediate cell-biomaterial interaction. - Highlights: • Composite silk fibroin-poly(L-lactic acid) scaffolds were obtained by electrospinning. • Intermolecular interactions between SF and PLLA were revealed for the first time. • Upon blending, the crystallisation of PLLA was hindered by the presence of SF. • SF crystallized preferentially and maintained its prevailing β-sheet structure. • The incorporation of SF into PLLA enhanced human keratinocytes adhesion and proliferation.

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

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

    2015-01-01

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

  12. The effect of strong intermolecular and chemical interactions on the compatibility of polymers

    Askadskii, Andrei A

    1999-01-01

    The data on compatibility and on the properties of polymer blends are generalised. The emphasis is placed on the formation of strong intermolecular interactions (dipole-dipole interaction and hydrogen bonding) between the components of blends, as well as on the chemical reactions between them. A criterion for the prediction of compatibility of polymers is described in detail. Different cases of compatibility are considered and the dependences of the glass transition temperatures on the composition of blends are analysed. The published data on the effect of strong intermolecular interactions between the blend components on the glass transition temperature are considered. The preparation of interpolymers is described whose macromolecules are composed of incompatible polymers, which leads to the so-called 'forced compatibility.' The bibliography includes 80 references.

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

    Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian

    2012-01-01

    to the axis perpendicular to the phenylacetylene plane and containing the center of mass. The calculated interaction energy is -418.9 cm(-1). To check further the potential, we obtain the rovibrational spectrum of the complex and the results are compared to the available experimental data. (C) 2012 American......We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set...... extended with a series of 3s3p2d1flg midbond functions. The potential is characterized by two equivalent global minima where the Ar atom is located above and below the phenylacetylene plane at a distance of 3.5781 angstrom from the molecular center of mass and at an angle of 9.08 degrees with respect...

  14. Pharmaceutical cocrystals, salts and multicomponent systems; intermolecular interactions and property based design.

    Berry, David J; Steed, Jonathan W

    2017-08-01

    As small molecule drugs become harder to develop and less cost effective for patient use, efficient strategies for their property improvement become increasingly important to global health initiatives. Improvements in the physical properties of Active Pharmaceutical Ingredients (APIs), without changes in the covalent chemistry, have long been possible through the application of binary component solids. This was first achieved through the use of pharmaceutical salts, within the last 10-15years with cocrystals and more recently coamorphous systems have also been consciously applied to this problem. In order to rationally discover the best multicomponent phase for drug development, intermolecular interactions need to be considered at all stages of the process. This review highlights the current thinking in this area and the state of the art in: pharmaceutical multicomponent phase design, the intermolecular interactions in these phases, the implications of these interactions on the material properties and the pharmacokinetics in a patient. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Dynamics of polymers in a good solvent - a molecular dynamics study using the Connection Machine

    Shannon, S.R.; Choy, T.C.

    1996-01-01

    In recent times the use of molecular dynamics simulations has become an important tool in modelling and understanding the dynamics of interacting many-body systems. With recent advances in computing power it is now feasible to perform modelling of systems which contain a large number of interacting particles, and thus to simulate the behaviour of real systems reasonably. Our earlier discoveries of anomalous corrections to scaling behaviour of the Edward's polymer were applied to study the dynamical behaviour of two dimensional polymer systems - either a single chain immersed in a fluid, a pure polymer melt, or with any concentration of polymers in the fluid. By choosing a suitable interaction potential between the fluid particles and the monomers, we are able to study the experimentally observable time dependent structure factor of polymers in a good solvent. Simulations were performed using the Connection Machine CM5 supercomputer at the Australian National University which due to its fast multi- processor nearest neighbour communications facility, enables us to easily model large systems of at least 3000 fluid plus monomer particles. Our study is based on a finite difference solution of Newton's equations of motion i.e. the Verlet algorithm, and the results are used to test current theories of polymer dynamics, which were based primarily on the earlier models proposed by Rouse (1953) and Zimm (1956). In particular dynamical scaling predictions is scrutinised to examine the effects due to the anomalous corrections-to-scaling behaviour found in an earlier work using finite-size scaling analysis of Monte-Carlo data and now understood via a new perturbation concept

  16. Intermolecular hydrogen bonds: From temperature-driven proton ...

    Abstract. We have combined neutron scattering and a range of numerical simulations to study hydrogen bonds in condensed matter. Two examples from a recent thesis will be presented. The first concerns proton transfer with increasing temperature in short inter- molecular hydrogen bonds [1,2]. These bonds have unique ...

  17. Quantitative analysis of intermolecular interactions in 2,2'-((4 ...

    SUBBIAH THAMOTHARAN

    2018-02-07

    Feb 7, 2018 ... in good agreement with the crystal structure of the title compound. The structures of title ... was isolated from the reaction medium by simple filtra- tion. Thus, a green protocol ... In this situation, a study to understand how other ...

  18. Influence of intermolecular interactions on the properties of carbon ...

    46

    Piotr Kamedulski , Anna Kaczmarek-Kedziera, Jerzy P. Lukaszewicz .... recent studies on this class of compounds/materials were predominantly .... Power 150 mW), Leica DM1300M camera Infinity 1; objective: Leica, N PLAN L50x/0.5).

  19. Role of quantitative and dynamic radioactive studies in renal testing

    Raynaud, C.

    1977-01-01

    Many dynamic and quantitative radioactive tests are at present used in studying renal function. Whether involving dynamic morphological tests such as sequential images, dynamic quantitative tests such as the renogram or quantitative static tests such as radioactive clearances, their effective and original contribution is rather unimportant. Only one provides original data, the Hg renal uptake test but it is generally avoided due to the radiation dose absorbed by the kidney in children. A study of the causes of this lack of effectiveness leads to the observation that such tests are not well adapted to the needs of kidneys specialists. They are for the most part based on replacing a 'cold' indicator by radioactive indicator and the advantages anticipated from using radionuclide are not evident. In fact, they are often cancelled by the shortcomings of external detection. For the future, it seems indispensable to abandon some traditional concepts which lead us to consider that the only exploitable renal function is represented by excretion. The kidney has other functions; one of the most interesting seems to be the function of uptake of heavy metals and toxic substances, a study of which is only possible using radionuclides. A new generation of radioactive tests based on a study of uptake and also on a study of other renal functions may provide dynamic or quantitative data which physician urgently need

  20. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

    Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

    2015-01-01

    Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

  1. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

  2. Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

    Shekhar, Adarsh

    Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

  3. Femtosecond photodissociation dynamics of I studied by ion imaging

    Larsen, J.J.; Bjerre, N.; Mørkbak, N.J.

    1998-01-01

    on imaging is employed to analyze the fragments from timed Coulomb explosion studies of femtosecond (fs) molecular dynamics. The technique provides high detection efficiency and direct recording of the two-dimensional velocity of all ionized fragments. We illustrate the approach by studying...... agreement with quantum mechanical wave packet simulations. We discuss the perspectives for extending the studies to photochemical reactions of small polyatomic molecules...

  4. Dynamical study of a laser with a saturable absorber

    Dignowity, D; RamIrez, R [Centro de Investigaciones en Optica, Loma del Bosque 115, Col. Lomas del Campestre, 37150, Leon, Guanajuato (Mexico)

    2005-01-01

    The study of a laser including a saturable absorber is presented. The non-linear system describing the complex dynamics of the laser is presented. The laser is shown to operate in several regimes depending on the parameters used. It is also shown how the control of the laser is possible depending on the operating regime parameters.

  5. A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

    AHLSTROM, P; BERENDSEN, HJC

    1993-01-01

    Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

  6. System Dynamic Modelling for a Balanced Scorecard: A Case Study

    Nielsen, Steen; Nielsen, Erland Hejn

    Purpose - The purpose of this research is to make an analytical model of the BSC foundation by using a dynamic simulation approach for a 'hypothetical case' model, based on only part of an actual case study of BSC. Design/methodology/approach - The model includes five perspectives and a number...

  7. Asymptotic study of a magneto-hydro-dynamic system

    Benameur, J.; Ibrahim, S.; Majdoub, M.

    2003-01-01

    In this paper, we study the convergence of solutions of a Magneto-Hydro-Dynamic system. On the torus T 3 , the proof is based on Schochet's methods, whereas in the case of the whole space R 3 , we use Strichartz's type estimates. (author)

  8. Spectroscopic studies of dynamically compacted monoclinic ZrO2

    Maczka, M.; Lutz, E.T.G.; Verbeek, H.J.; Oskam, K.; Meijerink, A.; Hanuza, J.; Stuivinga, M.E.C.

    1999-01-01

    The properties of dynamically compacted monoclinic zirconia have been studied by X-ray powder diffraction, IR, Raman, EPR and luminescence spectroscopy. Compaction introduces a large number of defects into the sample, which leads to a broadening of the X-ray lines, and IR and Raman bands. Besides,

  9. Charge-Transfer Complexes Studied by Dynamic Force Spectroscopy

    Jurriaan Huskens

    2013-03-01

    Full Text Available In this paper, the strength and kinetics of two charge-transfer complexes, naphthol-methylviologen and pyrene-methylviologen, are studied using dynamic force spectroscopy. The dissociation rates indicate an enhanced stability of the pyrene-methylviologen complex, which agrees with its higher thermodynamic stability compared to naphthol-methylviologen complex.

  10. Body dynamics and hydrodynamics of swimming larvae: a computational study

    Li, G.; Müller, U.K.; Leeuwen, van J.L.; Liu, H.

    2012-01-01

    To understand the mechanics of fish swimming, we need to know the forces exerted by the fluid and how these forces affect the motion of the fish. To this end, we developed a 3-D computational approach that integrates hydrodynamics and body dynamics. This study quantifies the flow around a swimming

  11. Planning Intervention Using Dynamic Assessments: A Case Study

    Hasson, Natalie; Dodd, Barbara

    2014-01-01

    Dynamic assessments (DA) of language have been shown to be a useful addition to the battery of tests used to diagnose language impairments in children, and to evaluate their skills. The current article explores the value of the information gained from a DA in planning intervention for a child with language impairment. A single case study was used…

  12. Molecular dynamics study on the relaxation properties of bilayered ...

    2017-08-31

    Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...

  13. Asymptotic study of a magneto-hydro-dynamic system

    Benameur, J [Institut Preparatoire aux Etudes d' Ingenieurs de Monastir (Tunisia); Ibrahim, S [Faculte des Sciences de Bizerte, Departement de Mathematiques, Bizerte (TN); [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)]. E-mail: slim.ibrahim@fsb.rnu.tn; Majdoub, M [Faculte des Sciences de Tunis, Departement de Mathematiques, Tunis (Tunisia)

    2003-01-01

    In this paper, we study the convergence of solutions of a Magneto-Hydro-Dynamic system. On the torus T{sup 3}, the proof is based on Schochet's methods, whereas in the case of the whole space R{sup 3}, we use Strichartz's type estimates. (author)

  14. Adsorption dynamics and equilibrium studies of Zn (II) onto chitosan

    Unknown

    Adsorption dynamics and equilibrium studies of Zn (II) onto chitosan. G KARTHIKEYAN*, K ANBALAGAN and N MUTHULAKSHMI ANDAL. Department of Chemistry, Gandhigram Rural Institute – Deemed University, Gandhigram 624 302, India e-mail: drg_karthikeyan@rediffmail.com. MS received 3 June 2003; revised 12 ...

  15. Fission dynamics as brought out in cold fragmentation studies

    Signarbieux, G.

    1986-10-01

    Fission dynamics problem has been addressed since the beginning. This paper is specifically concerned by ''even-odd effects '' in fragment distribution. These effects are reinterpreted, some complementary thoughts on double ionization chamber are given together with a study of fission dymanics at low energy [fr

  16. Recoil generated radiotracers in studies of molecular dynamics

    Spicer, L.D.

    1981-01-01

    This chapter summarizes many of the contributions that the recoil technique of generating excited radiotracer atoms in the presence of a thermal environment is making to the field of chemical dynamics. Specific topics discussed critically include characterization of the generation and behavior of excited molecules including fragmentation kinetics and energy transfer, measurement of thermal and hot kinetic parameters, and studies of reaction mechanisms and stereochemistry as a function of reaction energy. Distinctive features that provide unique approaches to dynamical problems are evaluated in detail and the complementarity with more conventional techniques is addressed. Prospects for future applications are also presented

  17. A study of dynamic filtration; Um estudo sobre filtracao dinamica

    Girao, Joaquim Helder S [PETROBRAS, Natal, RN (Brazil). Distrito de Perfuracao da Bacia Potiguar. Div. de Tecnicas de Perfuracao

    1990-12-31

    The problems that cause cost increase such as: formation damage and borehole swelling or caving lead us to study the filtration of the liquid part of formation drilling fluid. With the aim of comparing static and dynamic filtration rates, we developed a modest dynamic filtration equipment, consisting of a modified API filter, connected to reservoir by means of a positive injection pump. We carried out various tests, and the results were set in charts and tables. Through these, it is possible to notice how the static and dynamic filtration curves come apart for a same pressure value. We also evaluated the effects of circulation speed, starch concentration and counter pressure. This paper does not include calculations or mathematical models accounting for filtrate invasion radii, but it demonstrates, for example, that cleaning circulation will cause lower filtration rates at lower flows. (author) 5 refs., 11 figs., 14 tabs.

  18. A study of dynamic filtration; Um estudo sobre filtracao dinamica

    Girao, Joaquim Helder S. [PETROBRAS, Natal, RN (Brazil). Distrito de Perfuracao da Bacia Potiguar. Div. de Tecnicas de Perfuracao

    1989-12-31

    The problems that cause cost increase such as: formation damage and borehole swelling or caving lead us to study the filtration of the liquid part of formation drilling fluid. With the aim of comparing static and dynamic filtration rates, we developed a modest dynamic filtration equipment, consisting of a modified API filter, connected to reservoir by means of a positive injection pump. We carried out various tests, and the results were set in charts and tables. Through these, it is possible to notice how the static and dynamic filtration curves come apart for a same pressure value. We also evaluated the effects of circulation speed, starch concentration and counter pressure. This paper does not include calculations or mathematical models accounting for filtrate invasion radii, but it demonstrates, for example, that cleaning circulation will cause lower filtration rates at lower flows. (author) 5 refs., 11 figs., 14 tabs.

  19. Molecular dynamics study of atomic displacements in disordered solid alloys

    Puzyrev, Yevgeniy S.

    The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

  20. Study on dynamic behavior analysis of towed line array sensor

    Hyun Kyoung Shin

    2012-03-01

    Full Text Available A set of equations of motion is derived for vibratory motions of an underwater cable connected to a moving vehicle at one end and with drogues at the other end. From the static analysis, cable configurations are obtained for different vehicle speeds and towing pretensions are determined by fluid resistance of drogues. Also the dynamic analysis is required to predict its vibratory motion. Nonlinear fluid drag forces greatly influence the dynamic tension. In this study, a numerical analysis program was developed to find out the characteristic of cable behaviour. The motion is described in terms of space and time coordinates based on Chebyshev polynomial expansions. For the spatial integration the collocation method is employed and the Newmark method is applied for the time integration. Dynamic tensions, displacements, velocities, accelerations were predicted in the time domain while natural frequencies and transfer functions were obtained in the frequency domain.

  1. Dynamic study on digital cineangiography of acute digestive tract hemorrhage

    Yu Jianming; Feng Gansheng; Zeng Jun; Xu Caiyuan

    2000-01-01

    Objective: To study dynamically acute gastrointestinal tract hemorrhage with digital cine angiography. Methods: Fifty patients with acute gastrointestinal tract hemorrhage were performed with digital cineangiography and observed dynamically during arterial, capillary and venous phases. Results: Among 50 cases, there were positive results in 44 ones including gastrointestinal hemorrhage in 14, biliary hemorrhage in 2, splenic arterial bleeding in 3, left gastric arterial bleeding in 4, right gastroepiploic arterial bleeding in 5, SMA bleeding in 7 and IMA bleeding in 9.17 cases underwent a permanent embolization through artery and 11 with temporary embolization as well as 9 with infusion of hemostatic agent via artery. Conclusions: Serial digital cineangiogram can dynamically show acute digestive tract hemorrhage within different phase. It is helpful to detect the location and cause of hemorrhage

  2. Intermolecular energy transfer in binary systems of dye polymers

    Liu, Lin-I.; Barashkov, Nikolay N.; Palsule, Chintamani P.; Gangopadhyay, Shubhra; Borst, Walter L.

    2000-10-01

    We present results and physical interpretations for the energy transfer mechanisms in two-component dye polymer systems. The data consist of fluorescence emission spectra and decays. Two dyes were embedded in an epoxypolymer base, and only they participated in the energy transfer. Following pulsed laser excitation of the donor dye, energy transfer took place to the accept dye. The possible transfer paths considered here were nonradiative and radiative transfer. The latter involves two steps, emission and absorption of a photon, and therefore is relatively slow, while nonradiative transfer is a fast single step resulting from direct Coulomb interactions. A predominantly nonradiative transfer is desirable for applications, for instance in wavelength shifters in high energy particle detection. We studied the concentration effects of the dyes on the energy transfer and obtained the relative quantum efficiencies of various wavelength shifters from the fluorescence emission spectra. For low acceptor concentrations, radiative transfer was found to dominate, while nonradiative transfer became dominant at increasing dye concentrations. The fluorescence decays were analyzed with a sum-of-exponentials method and with Förster kinetics. The sum of exponential model yielded mean decay times of the dye polymers useful for a general classification. The decay times decreased as desired with increasing acceptor concentration. The samples, in which nonradiative energy transfer dominated, were analyzed with Förster kinetics. As a result, the natural decay times of the donor and acceptor dyes and the critical radii for nonradiative energy transfer were obtained from a global best fit.

  3. Rubrene: The interplay between intramolecular and intermolecular interactions determines the planarization of its tetracene core in the solid state

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

    2015-01-01

    exchange-repulsion interactions among the phenyl side groups. Calculations based on available crystallographic structures reveal that planar conformations of the tetracene core in the solid state result from intermolecular interactions that can be tuned

  4. Noncovalent Intermolecular Interactions in Organic Electronic Materials: Implications for the Molecular Packing vs Electronic Properties of Acenes

    Sutton, Christopher; Risko, Chad; Bredas, Jean-Luc

    2015-01-01

    Noncovalent intermolecular interactions, which can be tuned through the toolbox of synthetic chemistry, determine not only the molecular packing but also the resulting electronic, optical, and mechanical properties of materials derived from π

  5. Gold-catalyzed intermolecular coupling of sulfonylacetylene with allyl ethers: [3,3]- and [1,3]-rearrangements

    Jungho Jun

    2013-08-01

    Full Text Available Gold-catalyzed intermolecular couplings of sulfonylacetylenes with allyl ethers are reported. A cooperative polarization of alkynes both by a gold catalyst and a sulfonyl substituent resulted in an efficient intermolecular tandem carboalkoxylation. Reactions of linear allyl ethers are consistent with the [3,3]-sigmatropic rearrangement mechanism, while those of branched allyl ethers provided [3,3]- and [1,3]-rearrangement products through the formation of a tight ion–dipole pair.

  6. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

    Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

  7. Study of dynamic strain aging in dual phase steel

    Queiroz, R.R.U.; Cunha, F.G.G.; Gonzalez, B.M.

    2012-01-01

    Highlights: ► Characterization of the high temperature mechanical behavior of a dual phase steel. ► Determination of the effect of dynamic strain aging on the strain hardening rate. ► Identification of the mechanism associated with dynamic strain aging. ► The value of the interaction energy carbon–dislocation in ferrite was confirmed. - Abstract: The susceptibility to dynamic strain aging of a dual phase steel was evaluated by the variation of mechanical properties in tension with the temperature and the strain rate. The tensile tests were performed at temperatures varying between 25 °C and 600 °C and at strain rates ranging from 10 −2 to 5 × 10 −4 s −1 . The studied steel presented typical manifestations related to dynamic strain aging: serrated flow (the Portevin–Le Chatelier effect) for certain combinations of temperature and strain rates; the presence of a plateau in the variation of yield stress with temperature; a maximum in the curves of tensile strength, flow stress, and work hardening exponent as a function of temperature; and a minimum in the variation of total elongation with temperature. The determined apparent activation energy values, associated with the beginning of the Portevin–Le Chatelier effect and the maximum in the variation of flow stress with temperature, were 83 kJ/mol and 156 kJ/mol, respectively. These values suggest that the mechanism responsible for dynamic strain aging in the dual phase steel is the locking of dislocations by carbon atoms in ferrite and that the formation of clusters and/or transition carbides and carbide precipitation in martensite do not interfere with the dynamic strain aging process.

  8. The dynamics of physisorbed layers studied by neutron scattering

    Nielsen, M.; McTague, J.P.

    1978-01-01

    We discuss the neutron scattering technique applied to the study of adsorbed thin films. Despite the fact that neutrons are scattered very weakly by surfaces, recent studies have shown that both structural and dynamical information can be obtained even for submonolayer coverages. Results will be shown for films of Ar, D 2 , H 2 , and O 2 adsorbed on (001) surfaces of graphite and for H 2 molecules adsorbed on activated alumina. (orig.) [de

  9. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    Ratna Juwita

    2013-04-01

    Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.

  10. Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study

    Isaev, Olexandr; Kholod, Yana; Gorb, Leonid; Qasim, Mohammad; Fredrickson, Herb; Leszczynski, Jerzy

    2006-01-01

    .... In the present study molecular structure, electrostatic potential, vibrational spectrum and dynamics of thermal decomposition of CL-20 have been investigated by static and dynamic methods of ab...

  11. Study of hydrogen-molecule guests in type II clathrate hydrates using a force-matched potential model parameterised from ab initio molecular dynamics

    Burnham, Christian J.; Futera, Zdenek; English, Niall J.

    2018-03-01

    The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data.

  12. Statistical ensembles and molecular dynamics studies of anisotropic solids. II

    Ray, J.R.; Rahman, A.

    1985-01-01

    We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities

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

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

    2007-10-28

    Relativistic effects on the (129)Xe nuclear magnetic resonance shielding and (131)Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe(2) system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift delta, the anisotropy of the shielding tensor Deltasigma, and the NQC constant along the internuclear axis chi( parallel) are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Moller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for delta and Deltasigma by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for delta and Deltasigma in Xe(2). For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For chi( parallel), the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the (129)Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the

  14. High-speed AFM for Studying Dynamic Biomolecular Processes

    Ando, Toshio

    2008-03-01

    Biological molecules show their vital activities only in aqueous solutions. It had been one of dreams in biological sciences to directly observe biological macromolecules (protein, DNA) at work under a physiological condition because such observation is straightforward to understanding their dynamic behaviors and functional mechanisms. Optical microscopy has no sufficient spatial resolution and electron microscopy is not applicable to in-liquid samples. Atomic force microscopy (AFM) can visualize molecules in liquids at high resolution but its imaging rate was too low to capture dynamic biological processes. This slow imaging rate is because AFM employs mechanical probes (cantilevers) and mechanical scanners to detect the sample height at each pixel. It is quite difficult to quickly move a mechanical device of macroscopic size with sub-nanometer accuracy without producing unwanted vibrations. It is also difficult to maintain the delicate contact between a probe tip and fragile samples. Two key techniques are required to realize high-speed AFM for biological research; fast feedback control to maintain a weak tip-sample interaction force and a technique to suppress mechanical vibrations of the scanner. Various efforts have been carried out in the past decade to materialize high-speed AFM. The current high-speed AFM can capture images on video at 30-60 frames/s for a scan range of 250nm and 100 scan lines, without significantly disturbing week biomolecular interaction. Our recent studies demonstrated that this new microscope can reveal biomolecular processes such as myosin V walking along actin tracks and association/dissociation dynamics of chaperonin GroEL-GroES that occurs in a negatively cooperative manner. The capacity of nanometer-scale visualization of dynamic processes in liquids will innovate on biological research. In addition, it will open a new way to study dynamic chemical/physical processes of various phenomena that occur at the liquid-solid interfaces.

  15. Nitroxide stable radicals interacting as Lewis bases in hydrogen bonds: A search in the Cambridge structural data base for intermolecular contacts

    Alkorta, Ibon; Elguero, José; Elguero, Eric

    2017-11-01

    1125 X-ray structures of nitroxide free radicals presenting intermolecular hydrogen bonds have been reported in the Cambridge Structural Database. We will report in this paper a qualitative and quantitative analysis of these bonds. The observation in some plots of an excluded region was statistically analyzed using convex hull and kernel smooting methodologies. A theoretical study at the MP2 level with different basis has been carried out indicating that the nitronyl nitroxide radicals (five electrons) lie just in between nitroso compounds (four electrons) and amine N-oxides (six electrons) as far as hydrogen-bond basicity is concerned.

  16. A Numerical Study on Hydrodynamic Interactions between Dynamic Positioning Thrusters

    Jin, Doo Hwa; Lee, Sang Wook [University of Ulsan, Ulsan (Korea, Republic of)

    2017-06-15

    In this study, we conducted computational fluid dynamics (CFD) simulations for the unsteady hydrodynamic interaction of multiple thrusters by solving Reynolds averaged Navier-Stokes equations. A commercial CFD software, STAR-CCM+ was used for all simulations by employing a ducted thruster model with combination of a propeller and No. 19a duct. A sliding mesh technique was used to treat dynamic motion of propeller rotation and non-conformal hexahedral grid system was considered. Four different combinations in tilting and azimuth angles of the thrusters were considered to investigate the effects on the propulsion performance. We could find that thruster-hull and thruster-thruster interactions has significant effect on propulsion performance and further study will be required for the optimal configurations with the best tilting and relative azimuth angle between thrusters.

  17. Dynamic functional studies in nuclear medicine in developing countries

    1989-01-01

    The Proceedings document some of the trials and tribulations involved in setting up nuclear medicine facilities in general and specifically as regards nuclear medicine applications for the diagnosis of the diseases prevalent in the less developed countries. Most of the 51 papers deal with various clinical applications of dynamic functional studies. However, there was also a session on quality control of the equipment used, and a panel discussion critically looked at the problems and potential of dynamic studies in developing countries. This book will be of interest and use not only to those practising nuclear medicine in the developing countries, but it may also bring home to users in developed countries how ''more can be done with less''. Refs, figs and tabs

  18. A Dynamic Wind Generation Model for Power Systems Studies

    Estanqueiro, Ana

    2007-01-01

    In this paper, a wind park dynamic model is presented together with a base methodology for its application to power system studies. This detailed wind generation model addresses the wind turbine components and phenomena more relevant to characterize the power quality of a grid connected wind park, as well as the wind park response to the grid fast perturbations, e.g., low voltage ride through fault. The developed model was applied to the operating conditions of the selected sets of wind turbi...

  19. Dynamic capabilities and innovation: a Multiple-Case Study

    Bravo Ibarra, Edna Rocío; Mundet Hiern, Joan; Suñé Torrents, Albert

    2009-01-01

    After a detailed survey of the scientific literature, it was found that several characteristics of dynamic capabilities were similar to those of innovation capability. Therefore, with a deeper study of the first ones, it could be possible to design a model aimed to structure innovation capability. Thus, this work presents a conceptual model, where the innovation capability is shown as result of three processes: knowledge absorption and creation capability, knowledge integration and knowledge ...

  20. Dynamic Aperture Studies for the FCC-ee

    Medina, L; Tomas, R; Zimmermann, F

    2015-01-01

    Dynamic aperture (DA) studies have been conducted on the latest Future Circular Collider – ee (FCC-ee) lattices as a function of momentum deviation.Two different schemes for the interaction region are used, which are connected to the main arcs: the crab waist approach, developed by BINP, and an update to the CERN design where the use of crab cavities is envisioned. The results presented show an improvement in the performance of both designs.

  1. Water Tunnel Studies of Dynamic Wing Flap Effects

    2016-06-01

    NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release; distribution is unlimited WATER TUNNEL...Master’s Thesis 4. TITLE AND SUBTITLE WATER TUNNEL STUDIES OF DYNAMIC WING FLAP EFFECTS 5. FUNDING NUMBERS 6. AUTHOR(S) Edgar E. González 7. PERFORMING...ABSTRACT (maximum 200 words ) The flow features developing over a two-element NACA 0012 airfoil, with the rear portion serving as a trailing edge flap

  2. Dynamic Aperture Studies for the LHC High Luminosity Lattice

    De Maria, R; Giovannozzi, Massimo; Mcintosh, Eric; Cai, Y; Nosochkov, Y; Wang, M H

    2015-01-01

    Since quite some time, dynamic aperture studies have been undertaken with the aim of specifying the required field quality of the new magnets that will be installed in the LHC ring in the framework of the high-luminosity upgrade. In this paper the latest results concerning the specification work will be presented, taking into account both injection and collision energies and the field quality contribution from all the magnets in the newly designed interaction regions.

  3. Numerical study of the initial dynamics in tormac

    Aydemir, A.Y.

    1979-01-01

    Using a single fluid magnetohydrodynamic (MHD) code, we study the initial plasma dynamics in Tormac, an experimental device which attempts to confine plasma in a toroidal, two-pole cusp field. The code is in two dimensions and includes classical electrical conductivity and a constant heat conductivity. The full set of nonlinear MHD equations for the mass density, fluid velocity, temperature, the poloidal flux function, and the poloidal current function are solved using a predictor-corrector method

  4. Studies of network organization and dynamics of e-beam crosslinked PVPs: From macro to nano

    Dispenza, C.; Grimaldi, N.; Sabatino, M.-A.; Todaro, S.; Bulone, D.; Giacomazza, D.; Przybytniak, G.; Alessi, S.; Spadaro, G.

    2012-01-01

    In this work the influence of poly(N-vinyl pyrrolidone) (PVP) concentration in water on the organization and dynamics of the corresponding macro-/nanogel networks has been systematically investigated. Irradiation has been performed at the same irradiation dose (within the sterilization dose range) and dose rate. In the selected irradiation conditions, the transition between macroscopic gelation and micro-/nanogels formation is observed just below the critical overlap concentration (∼1 wt%), whereas the net prevalence of intra-molecular over inter-molecular crosslinking occurs at a lower polymer concentration (below 0.25 wt%). Dynamic–mechanical spectroscopy has been applied as a classical methodology to estimate the network mesh size for macrogels in their swollen state, while 13 C NMR spin–lattice relaxation spectroscopy has been applied on both the macrogel and nanogel freeze dried residues to withdraw interesting information of the network spatial organization in the passage of scale from macro to nano. - Highlights: ► Aqueous solutions of commercial PVP were irradiated using linear electron accelerator. ► By varying polymer concentration it is possible to obtain information from macro to nano networks. ► Spin–lattice relaxation times are associated to the mobility of molecular segments. ► 1 H– 13 C-NMR proton relaxation time represents a junction between macro/nano world.

  5. Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies

    Simon, A.; Rapacioli, M.; Rouaut, G.; Trinquier, G.; Gadéa, F. X.

    2017-03-01

    We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

  6. Physical properties of Cu nanoparticles: A molecular dynamics study

    Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.

    2014-01-01

    Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index

  7. Dynamic behavior of hybrid sodium bearings. Theoretical and experimental studies

    Guidez, J.; Juignet, N.; Queval, M.

    1981-08-01

    The primary sodium pump shaft lower section of a fast breeder reactor is guided by a hydrostatic sodium bearing. This recess type bearing is supplied via orifices restrictors. Sodium is sampled at hight pressure at the diffuser outlet and is then centrifuged towards the orifices restrictors. Bearing stiffness and damping data is essential for the study of rotor dynamic behavior. Two points in particular may then be studied: - calculation of rotor instability ranges and critical speeds, - dynamic behavior of the rotor in the event of an earthquake. As regards the bearing design, the problem is to obtain the pressure fields in the liquid film. The integration of these pressure fields will then give the stiffness coefficients. The damping coefficients can then be obtained by the same calculation after slight displacement. The Reynolds equation can be used to study the liquid film (under any conditions for the turbulent and inertia effects). Then the computer code DELPAL is explained that solves the modified Reynolds equation using a finite element method. The presentation of tests conducted in 1981 on the Super-Phenix 1 full scall bearing (diameter 850 mm) in water is made. In conclusion this paper describes a method for calculating the stiffness and damping matrices of a hydrostatic bearing using the DELPAL calculation code and shows the loop of behavior tests on a bearing with sinusoidal excitation. The results, obtained by calculation and by testing, are indispensable when calculating the dynamic behavior of the shaft line

  8. Parameter study on dynamic behavior of ITER tokamak scaled model

    Nakahira, Masataka; Takeda, Nobukazu

    2004-12-01

    This report summarizes that the study on dynamic behavior of ITER tokamak scaled model according to the parametric analysis of base plate thickness, in order to find a reasonable solution to give the sufficient rigidity without affecting the dynamic behavior. For this purpose, modal analyses were performed changing the base plate thickness from the present design of 55 mm to 100 mm, 150 mm and 190 mm. Using these results, the modification plan of the plate thickness was studied. It was found that the thickness of 150 mm gives well fitting of 1st natural frequency about 90% of ideal rigid case. Thus, the modification study was performed to find out the adequate plate thickness. Considering the material availability, transportation and weldability, it was found that the 300mm thickness would be a limitation. The analysis result of 300mm thickness case showed 97% fitting of 1st natural frequency to the ideal rigid case. It was however found that the bolt length was too long and it gave additional twisting mode. As a result, it was concluded that the base plate thickness of 150mm or 190mm gives sufficient rigidity for the dynamic behavior of the scaled model. (author)

  9. Morse-Morse-Spline-Van der Waals intermolecular potential suitable for hexafluoride gases

    Coroiu, Ilioara

    2004-01-01

    Several effective isotopic pair potential functions have been proposed to characterize the bulk properties of quasispherical molecules, in particular the hexafluorides, but none got a success. Unfortunately, these potentials have repulsive walls steeper than those which describe the hexafluorides. That these intermolecular potentials are not quite adequate is shown by the lack of complete agreement between theory and experiment even for the rare gases. Not long ago, R. A. Aziz et al. have constructed a Morse-Morse-Spline-Van der Waals (MMSV) potential. The MMSV potential incorporates the determination of C 6 dispersion coefficient and it reasonably correlates second virial coefficients and viscosity data of sulphur hexafluoride at the same time. None of the potential functions previously proposed in literature could predict these properties simultaneously. We calculated the second virial coefficients and a large number of Chapman-Cowling collision integrals for this improved intermolecular potential, the MMSV potential. The results were tabulated for a large reduced temperature range, kT/ε from 0.1 to 100. The treatment was entirely classical and no corrections for quantum effects were made. The higher approximations to the transport coefficients and the isotopic thermal diffusion factor were also calculated and tabulated for the same range. In this paper we present the evaluation of the uranium hexafluoride potential parameters for the MMSV intermolecular potential. To find a single set of potential parameters which could predict all the transport properties (viscosity, thermal conductivity, self diffusion, etc.), as well as the second virial coefficients, simultaneously, the method suggested by Morizot and a large assortment of literature data were used. Our results emphasized that the Morse-Morse-Spline-Van der Waals potential have the best overall predictive ability for gaseous hexafluoride data, certain for uranium hexafluoride. (author)

  10. A qualitative numerical study of high dimensional dynamical systems

    Albers, David James

    Since Poincare, the father of modern mathematical dynamical systems, much effort has been exerted to achieve a qualitative understanding of the physical world via a qualitative understanding of the functions we use to model the physical world. In this thesis, we construct a numerical framework suitable for a qualitative, statistical study of dynamical systems using the space of artificial neural networks. We analyze the dynamics along intervals in parameter space, separating the set of neural networks into roughly four regions: the fixed point to the first bifurcation; the route to chaos; the chaotic region; and a transition region between chaos and finite-state neural networks. The study is primarily with respect to high-dimensional dynamical systems. We make the following general conclusions as the dimension of the dynamical system is increased: the probability of the first bifurcation being of type Neimark-Sacker is greater than ninety-percent; the most probable route to chaos is via a cascade of bifurcations of high-period periodic orbits, quasi-periodic orbits, and 2-tori; there exists an interval of parameter space such that hyperbolicity is violated on a countable, Lebesgue measure 0, "increasingly dense" subset; chaos is much more likely to persist with respect to parameter perturbation in the chaotic region of parameter space as the dimension is increased; moreover, as the number of positive Lyapunov exponents is increased, the likelihood that any significant portion of these positive exponents can be perturbed away decreases with increasing dimension. The maximum Kaplan-Yorke dimension and the maximum number of positive Lyapunov exponents increases linearly with dimension. The probability of a dynamical system being chaotic increases exponentially with dimension. The results with respect to the first bifurcation and the route to chaos comment on previous results of Newhouse, Ruelle, Takens, Broer, Chenciner, and Iooss. Moreover, results regarding the high

  11. The same number of optimized parameters scheme for determining intermolecular interaction energies

    Kristensen, Kasper; Ettenhuber, Patrick; Eriksen, Janus Juul

    2015-01-01

    We propose the Same Number Of Optimized Parameters (SNOOP) scheme as an alternative to the counterpoise method for treating basis set superposition errors in calculations of intermolecular interaction energies. The key point of the SNOOP scheme is to enforce that the number of optimized wave...... as numerically. Numerical results for second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster with single, double, and approximate triple excitations (CCSD(T)) show that the SNOOP scheme in general outperforms the uncorrected and counterpoise approaches. Furthermore, we show that SNOOP...

  12. Dynamic viscosity study of barley malt and chicory concentrates

    G. O. Magomedov

    2016-01-01

    Full Text Available The purpose of research is to find optimal conditions for dispersing and subsequent dehydration of liquid food environments in the nozzle spray drying chamber through the study of dynamic changes in viscosity according to temperature, velocities gradients and dry residue content. The objects of study were roasted chicory and malt barley concentrates with dry residue content of 20, 40, 60 and 80%. Research of dynamic viscosity were carried out at the measuring complex based on the rotational viscometer Rheotest II, analog-to-digital converter, module Laurent and a personal computer with a unique software that allows to record in real time (not only on a tape recorder, but also in the form of graphic files the behavior of the viscosity characteristics of concentrates. Registration of changes of dynamic viscosity was carried out at a shear rate gradient from 1,0 с -1 to 27,0 с -1 and the products temperature thermostating : 35, 55, 75˚ C. The research results are presented in the form of graphic dependences of effective viscosity on shear rate and flow curves (dependencies of shear stresses on the velocity gradient, which defined flow regimes, the optimal modes of dispersion concentrates into spray dryer chambers in obtaining of powdered semi-finished products and instanting were found: dry residue content - 40 %, concentrate temperature - 75 ˚C, velocity gradient in the air channel of the nozzle at least 20 c-1

  13. Dynamic modelling and experimental study of cantilever beam with clearance

    Li, B; Jin, W; Han, L; He, Z

    2012-01-01

    Clearances occur in almost all mechanical systems, typically such as the clearance between slide plate of gun barrel and guide. Therefore, to study the clearances of mechanisms can be very important to increase the working performance and lifetime of mechanisms. In this paper, rigid dynamic modelling of cantilever with clearance was done according to the subject investigated. In the rigid dynamic modelling, clearance is equivalent to the spring-dashpot model, the impact of beam and boundary face was also taken into consideration. In ADAMS software, the dynamic simulation was carried out according to the model above. The software simulated the movement of cantilever with clearance under external excitation. Research found: When the clearance is larger, the force of impact will become larger. In order to study how the stiffness of the cantilever's supporting part influences natural frequency of the system, A Euler beam which is restricted by a draught spring and a torsion spring at its end was raised. Through numerical calculation, the relationship between natural frequency and stiffness was found. When the value of the stiffness is close to the limit value, the corresponding boundary condition is illustrated. An ADAMS experiment was carried out to check the theory and the simulation.

  14. Granulometry use for the study of dynamics speckles patterns

    Mavilioa, Adriana; Fernandez, Margarita; Trivi, Marcelo; Rabal, Hector; Arizaga, Ricardo

    2009-01-01

    Dynamic speckle patterns are generated by laser light scattering on surfaces that exhibit some kind of activity, due to physical or biological processes that take place in the illuminated object. The characterization of this dynamic process is carried out by studying the texture changes of auxiliary images: temporal history of the speckle pattern (THSP) obtained from this speckles patterns. The drying process of water borne paint is studied through a method based on mathematical morphology applied to the THSP image processing. It is based on obtaining the granulometry of these images and their characteristic granulometric spectrum. From the granulometric size distribution of each THSP image four parameters are obtained: mean length, standard deviation, asymmetry and kurtosis. These parameters are found to be suitable as texture features. The Mahalanobis distance is calculated between the texture features of the THSP images representative of the temporary stages of the drying process and the features of the final stage or pattern texture. The behavior of the distance function describes satisfactorily the drying process of the water borne paint. Finally, these results are compared with the obtained by other methods. Compared with others, the granulometric method reported in this work distinguished by its simplicity and easy implementation and can be used to characterize the evolution of any process recorded through dynamic speckles. (Author)

  15. Application of Solution NMR Spectroscopy to Study Protein Dynamics

    Christoph Göbl

    2012-03-01

    Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.

  16. Dynamic modelling and experimental study of cantilever beam with clearance

    Li, B.; Jin, W.; Han, L.; He, Z.

    2012-05-01

    Clearances occur in almost all mechanical systems, typically such as the clearance between slide plate of gun barrel and guide. Therefore, to study the clearances of mechanisms can be very important to increase the working performance and lifetime of mechanisms. In this paper, rigid dynamic modelling of cantilever with clearance was done according to the subject investigated. In the rigid dynamic modelling, clearance is equivalent to the spring-dashpot model, the impact of beam and boundary face was also taken into consideration. In ADAMS software, the dynamic simulation was carried out according to the model above. The software simulated the movement of cantilever with clearance under external excitation. Research found: When the clearance is larger, the force of impact will become larger. In order to study how the stiffness of the cantilever's supporting part influences natural frequency of the system, A Euler beam which is restricted by a draught spring and a torsion spring at its end was raised. Through numerical calculation, the relationship between natural frequency and stiffness was found. When the value of the stiffness is close to the limit value, the corresponding boundary condition is illustrated. An ADAMS experiment was carried out to check the theory and the simulation.

  17. Dynamic SEM wear studies of tungsten carbide cermets

    Brainard, W. A.; Buckley, D. H.

    1975-01-01

    Dynamic friction and wear experiments were conducted in a scanning electron microscope. The wear behavior of pure tungsten carbide and composite with 6 and 15 weight percent cobalt binder was examined. Etching of the binder was done to selectively determine the role of the binder in the wear process. Dynamic experiments were conducted as the WC and bonded WC cermet surfaces were transversed by a 50 micron radiused diamond stylus. These studies show that the predominant wear process in WC is fracture initiated by plastic deformation. The wear of the etched cermets is similar to pure WC. The presence of the cobalt binder reduces both friction and wear. The cementing action of the cobalt reduces granular separation and promotes a dense polished layer because of its low shear strength film-forming properties. The wear debris generated from unetched surface is approximately the same composition as the bulk.

  18. Time-resolved infrared studies of protein conformational dynamics

    Woodruff, W.H.; Causgrove, T.P.; Dyer, R.B. [Los Alamos National Laboratory, NM (United States); Callender, R.H. [Univ. of New York, NY (United States)

    1994-12-01

    We have demonstrated that TRIR in the amide I region gives structural information regarding protein conformational changes in realtime, both on processes involved in the development of the functional structure (protein folding) and on protein structural changes that accompany the functional dynamics of the native structure. Assignment of many of the amide I peaks to specific amide or sidechain structures will require much additional effort. Specifically, the congestion and complexity of the protein vibrational spectra dictate that isotope studies are an absolute requirement for more than a qualitative notion of the structural interpretation of these measurements. It is clear, however, that enormous potential exists for elucidating structural relaxation dynamics and energetics with a high degree of structural specificity using this approach.

  19. NATO Advanced Study Institute on Hamiltonian Dynamical Systems and Applications

    2008-01-01

    Physical laws are for the most part expressed in terms of differential equations, and natural classes of these are in the form of conservation laws or of problems of the calculus of variations for an action functional. These problems can generally be posed as Hamiltonian systems, whether dynamical systems on finite dimensional phase space as in classical mechanics, or partial differential equations (PDE) which are naturally of infinitely many degrees of freedom. This volume is the collected and extended notes from the lectures on Hamiltonian dynamical systems and their applications that were given at the NATO Advanced Study Institute in Montreal in 2007. Many aspects of the modern theory of the subject were covered at this event, including low dimensional problems as well as the theory of Hamiltonian systems in infinite dimensional phase space; these are described in depth in this volume. Applications are also presented to several important areas of research, including problems in classical mechanics, continu...

  20. Dissolution Dynamic Nuclear Polarization capability study with fluid path

    Malinowski, Ronja Maja; Lipsø, Hans Kasper Wigh; Lerche, Mathilde Hauge

    2016-01-01

    Signal enhancement by hyperpolarization is a way of overcoming the low sensitivity in magnetic resonance; MRI in particular. One of the most well-known methods, dissolution Dynamic Nuclear Polarization, has been used clinically in cancer patients. One way of ensuring a low bioburden of the hyperp......Signal enhancement by hyperpolarization is a way of overcoming the low sensitivity in magnetic resonance; MRI in particular. One of the most well-known methods, dissolution Dynamic Nuclear Polarization, has been used clinically in cancer patients. One way of ensuring a low bioburden...... of the hyperpolarized product is by use of a closed fluid path that constitutes a barrier to contamination. The fluid path can be filled with the pharmaceuticals, i.e. imaging agent and solvents, in a clean room, and then stored or immediately used at the polarizer. In this study, we present a method of filling...

  1. Empirical study on social groups in pedestrian evacuation dynamics

    von Krüchten, Cornelia; Schadschneider, Andreas

    2017-06-01

    Pedestrian crowds often include social groups, i.e. pedestrians that walk together because of social relationships. They show characteristic configurations and influence the dynamics of the entire crowd. In order to investigate the impact of social groups on evacuations we performed an empirical study with pupils. Several evacuation runs with groups of different sizes and different interactions were performed. New group parameters are introduced which allow to describe the dynamics of the groups and the configuration of the group members quantitatively. The analysis shows a possible decrease of evacuation times for large groups due to self-ordering effects. Social groups can be approximated as ellipses that orientate along their direction of motion. Furthermore, explicitly cooperative behaviour among group members leads to a stronger aggregation of group members and an intermittent way of evacuation.

  2. Molecular dynamics studies of the melting of butane and hexane monolayers adsorbed on the basal-plane surface of graphite

    Hansen, Flemming Yssing; Newton, J. C.; Taub, H.

    1993-01-01

    The effect of molecular steric properties on the melting of quasi-two-dimensional solids is investigated by comparing results of molecular dynamics simulations of the melting of butane and hexane monolayers adsorbed on the basal-plane surface of graphite. These molecules differ only in their length......, being members of the n-alkane series [CH3(CH2)n−2CH3] where n=4 for butane and n=6 for hexane. The simulations employ a skeletal model, which does not include the hydrogen atoms explicitly, to represent the intermolecular and molecule–substrate interactions. Nearest-neighbor intramolecular bonds...... are fixed in length, but the molecular flexibility is preserved by allowing the bend and dihedral torsion angles to vary. The simulations show a qualitatively different melting behavior for the butane and hexane monolayers consistent with neutron and x-ray scattering experiments. The melting of the low...

  3. Molecular dynamics study of lubricant depletion by pulsed laser heating

    Seo, Young Woo; Rosenkranz, Andreas; Talke, Frank E.

    2018-05-01

    In this study, molecular dynamics simulations were performed to numerically investigate the effect of pulsed laser heating on lubricant depletion. The maximum temperature, the lubricant depletion width, the number of evaporated lubricant beads and the number of fragmented lubricant chains were studied as a function of laser peak power, pulse duration and repetition rate. A continuous-wave laser and a square pulse laser were simulated and compared to a Gaussian pulse laser. With increasing repetition rate, pulsed laser heating was found to approach continuous-wave laser heating.

  4. Ti and Zr surfaces studied by molecular dynamics

    Pascuet, Maria I.; Passianot, Roberto C.; Monti, Ana M.

    2003-01-01

    The interaction between point defects technique and the (0001), (1-210), (10-10) surfaces in Ti and Zr is studied by the molecular dynamics technique. Both of metals are in the hexagonal structure and within a temperature range of 100 to 900 K. The atomic interactions are modeled by EAM-type many-body potentials, that were used previously in static simulations. New migration mechanisms are unraveled and others are verified with respect to those already proposed in the static studies. Also included is an analysis of the vacancy stability in the sub-surface layers of the prismatic surfaces. (author)

  5. Ion Dynamics Study of Potato Starch + Sodium Salts Electrolyte System

    Tuhina Tiwari

    2013-01-01

    Full Text Available The effect of different anions, namely, SCN−, I−, and ClO4−, on the electrical properties of starch-based polymer electrolytes has been studied. Anion size and conductivity are having an inverse trend indicating systems to be predominantly anionic conductor. Impact of anion size and multiplet forming tendency is reflected in number of charge carriers and mobility, respectively. Ion dynamics study reveals the presence of different mechanisms in different frequency ranges. Interestingly, superlinear power law (SLPL is found to be present at <5 MHz frequency, which is further confirmed by dielectric data.

  6. Spectroscopic and dynamical studies of highly energized small polyatomic molecules

    Field, R.W.; Silbey, R.J. [Massachusetts Institute of Technology, Cambridge (United States)

    1993-12-01

    The authors have initiated a program to perform spectroscopic and dynamic studies of small molecules. Large amplitude motions in excited acetylene were discussed along with plans to record the dispersed fluorescence (DF) and the stimulated emission pumping (SEP) spectra. SEP spectra were reported for the formyl radical. A Fourier transform spectrometer was discussed with respect to its ability to probe the structure of radicals. This instrument is capable of performing studies using various techniques such as magnetic rotation spectroscopy and sub-Doppler sideband-OODR Zeman (SOODRZ) spectroscopy.

  7. Numerical analysis of data in dynamic function studies

    Riihimaeki, E.

    1975-01-01

    Relations between tracer theories, models for organ function and the numerical solution of parameters from tracer experiments are reviewed. A unified presentation is given in terms of systems theory. Dynamic tracer studies should give the flow and volume of the tracer and, possibly, indications of the internal structure of the organ studied. Proper program writing will facilitate the exchange of the programs between the users and thereby avoid duplication of effort. An important attribute in this respect is machine independence of the programs which is achieved by the use of a high-level language. (author)

  8. Photocatalytic oxidation dynamics of acetone on TiO2: tight-binding quantum chemical molecular dynamics study

    Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

    2005-01-01

    The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed

  9. Molecular dynamics studies of transport properties and equation of state of supercritical fluids

    Nwobi, Obika C.

    Many chemical propulsion systems operate with one or more of the reactants above the critical point in order to enhance their performance. Most of the computational fluid dynamics (CFD) methods used to predict these flows require accurate information on the transport properties and equation of state at these supercritical conditions. This work involves the determination of transport coefficients and equation of state of supercritical fluids by equilibrium molecular dynamics (MD) simulations on parallel computers using the Green-Kubo formulae and the virial equation of state, respectively. MD involves the solution of equations of motion of a system of molecules that interact with each other through an intermolecular potential. Provided that an accurate potential can be found for the system of interest, MD can be used regardless of the phase and thermodynamic conditions of the substances involved. The MD program uses the effective Lennard-Jones potential, with system sizes of 1000-1200 molecules and, simulations of 2,000,000 time-steps for computing transport coefficients and 200,000 time-steps for pressures. The computer code also uses linked cell lists for efficient sorting of molecules, periodic boundary conditions, and a modified velocity Verlet algorithm for particle displacement. Particle decomposition is used for distributing the molecules to different processors of a parallel computer. Simulations have been carried out on pure argon, nitrogen, oxygen and ethylene at various supercritical conditions, with self-diffusion coefficients, shear viscosity coefficients, thermal conductivity coefficients and pressures computed for most of the conditions. Results compare well with experimental and the National Institute of Standards and Technology (NIST) values. The results show that the number of molecules and the potential cut-off radius have no significant effect on the computed coefficients, while long-time integration is necessary for accurate determination of the

  10. Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies.

    Anda, André; De Vico, Luca; Hansen, Thorsten

    2017-06-08

    Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.

  11. Intermolecular cope-type hydroamination of alkenes and alkynes using hydroxylamines.

    Moran, Joseph; Gorelsky, Serge I; Dimitrijevic, Elena; Lebrun, Marie-Eve; Bédard, Anne-Catherine; Séguin, Catherine; Beauchemin, André M

    2008-12-31

    The development of the Cope-type hydroamination as a method for the metal- and acid-free intermolecular hydroamination of hydroxylamines with alkenes and alkynes is described. Aqueous hydroxylamine reacts efficiently with alkynes in a Markovnikov fashion to give oximes and with strained alkenes to give N-alkylhydroxylamines, while unstrained alkenes are more challenging. N-Alkylhydroxylamines also display similar reactivity with strained alkenes and give modest to good yields with vinylarenes. Electron-rich vinylarenes lead to branched products while electron-deficient vinylarenes give linear products. A beneficial additive effect is observed with sodium cyanoborohydride, the extent of which is dependent on the structure of the hydroxylamine. The reaction conditions are found to be compatible with common protecting groups, free OH and NH bonds, as well as bromoarenes. Both experimental and theoretical results suggest the proton transfer step of the N-oxide intermediate is of vital importance in the intermolecular reactions of alkenes. Details are disclosed concerning optimization, reaction scope, limitations, and theoretical analysis by DFT, which includes a detailed molecular orbital description for the concerted hydroamination process and an exhaustive set of calculated potential energy surfaces for the reactions of various alkenes, alkynes, and hydroxylamines.

  12. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2013-09-01

    In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the 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 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

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

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2014-06-01

    In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-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 Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  14. A general intermolecular force field based on tight-binding quantum chemical calculations

    Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

    2017-10-01

    A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

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

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

    2013-06-01

    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.

  16. Photophysical and computational investigation of the intermolecular interactions of pyrene with phenothiazine and promazine

    Güloğlu, Pınar; Acar, Nursel, E-mail: nursel.acar@ege.edu.tr

    2016-10-20

    Highlights: • Intermolecular interactions of pyrene with phenothiazine/promazine were investigated. • All investigated systems were optimized at ωB97XD/6-31G(d,p) level in gas phase. • The electronic transitions were determined using frontier orbitals. • Both Py–Pheno and Py–Prom are potential candidates for charge transfer systems. - Abstract: The intermolecular interactions between the pyrene (Py) (as acceptor) and phenothiazine (Pheno), promazine (Prom) (as donors) were investigated using UV/Vis absorption and fluorescence spectroscopy. Fluorescence quenching rate constants for Py–Pheno and Py–Prom systems have been calculated approximately 10{sup 10} M{sup −1} s{sup −1}, indicating diffusion controlled processes. A computational investigation has also been carried out in gas phase at ωB97XD/6-31G(d,p) level. Time-dependent density functional theory (TDDFT) was used to calculate the electronic transitions of molecules at B3LYP/6-311++G(d,p) level. Total electronic energies, complexation energies, free energy differences, excitation wavelengths, and HOMO–LUMO energy gaps are discussed in gas phase. Analyses of first excited singlet states have indicated charge transfers transitions between Py and Pheno, Prom through π–π stacking in gas phase at 433 nm and 466 nm, respectively. Due to its charge transfer character, Py–Pheno and Py–Prom systems seem to be appropriate models to investigate and design photosensitive materials.

  17. Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations

    Hansen, Sara Krogh; Vestergaard, Mikkel; Thøgersen, Lea

    2014-01-01

    , for example, order parameters. Therefore, valuable insight into the dynamics of biomolecules may be achieved by the present method. We have applied this method to study the dynamics of lipid bilayers containing the antimicrobial peptide alamethicin, and we show that the calculated 31P spectra obtained...

  18. Experimental study of dynamic stall on Darrieus wind turbine blades

    Brochier, G.; Fraunie, P.; Beguier, C.; Paraschivoiu, I.

    1985-12-01

    An experimental study of periodic vortex phenomena was performed on a model of a two straight-bladed Darrieus wind turbine under controlled-rotation conditions in the IMST water tunnel. The main focus of interest was the tip-speed ratios at which dynamic stall appears. Observations of this phenomenon from dye emission and the formation of hydrogen bubbles were made in the form of photographs, film and video recordings. Velocity measurements were obtained using the Laser-Doppler Velocimeter and components of velocity fluctuations could be determined quantitatively.

  19. Study on Dynamic Characteristics of Microbial Enhanced Oil Recovery

    Zhao, Yang; Shi, Fang; Qin, Wuying; Yan, Jing

    2018-01-01

    With the rapid development of economy, the demand for oil is increasing day by day. MEOR has the advantages of low cost and no pollution to the environment, attracted widespread attention. In this paper, the dynamic characteristics of microbial enhanced oil recovery were studied by laboratory experiments. The result showed that all the microbial flooding recovery rate could reach more than 5%, and the total recovery could reach more than 35% and if the injection period of microbial composite system was advanced, the whole oil displacement process could be shortened and the workload would be reduced.

  20. Loading technique for dynamic response studies of geological materials

    Butler, R.I.; Forrestal, M.J.

    1979-04-01

    A loading technique to study the dynamic response of tuff was explored. Loading is provided by electrically exploding etched copper mesh patterns with current from a capacitor discharge. Pressure pulses with peak pressures up to 1.25 kbar and 0.10 to 0.20 ms durations were measured with a pressure bar. The upper value of peak pressure was limited by the strength of the experimental apparatus, and higher pressure generation is possible with a redesign of test hardware. 6 figures, 2 tables

  1. Highly Resolved Studies of Vacuum Ultraviolet Photoionization Dynamics

    Kakar, Sandeep

    We use measurements of dispersed fluorescence from electronically excited photoions to study fundamental aspects of intramolecular dynamics. Our experimental innovations make it possible to obtain highly resolved photoionization data that offer qualitative insights into molecular scattering. In particular, we obtain vibrationally resolved data to probe coupling between the electronic and nuclear degrees of freedom by studying the distribution of vibrational energy among photoions. Vibrationally resolved branching ratios are measured over a broad spectral range of excitation energy and their non-Franck-Condon behavior is used as a tool to investigate two diverse aspects of shape resonant photoionization. First, vibrational branching ratios are obtained for the SiF_4 5a _1^{-1} and CS_2 5sigma_{rm u} ^{-1} photoionization channels to help elucidate the microscopic aspects of shape resonant wavefunction for polyatomic molecules. It is shown that in such molecules the shape resonant wavefunction is not necessarily attributable to a specific bond in the molecule. Second, the multichannel aspect of shape resonant photoionization dynamics, reflected in continuum channel coupling, is investigated by obtaining vibrational branching ratios for the 2 sigma_{rm u}^{ -1} and 4sigma^{ -1} photoionization of the isoelectronic molecules N_2 and CO, respectively. These data indicate that effects of continuum coupling may be widespread. We also present the first set of rotationally resolved data over a wide energy range for the 2 sigma_{rm u}^{ -1} photoionization of N_2. These data probe the partitioning of the angular momentum between the photoelectron and photoion, and highlight the multicenter nature of the molecular potential. These case studies illustrate the utility of dispersed fluorescence measurements as a complement to photoelectron spectroscopy for obtaining highly resolved data for molecular photoionization. These measurements makes it possible to probe intrinsically

  2. What about getting physiological information into dynamic gamma camera studies

    Kiuru, A.; Nickles, R. J.; Holden, J. E.; Polcyn, R. E.

    1976-01-01

    A general technique has been developed for the multiplexing of time dependent analog signals into the individual frames of a gamma camera dynamic function study. A pulse train, frequency-modulated by the physiological signal, is capacitively coupled to the preamplifier servicing anyone of the outer phototubes of the camera head. These negative tail pulses imitate photoevents occuring at a point outside of the camera field of view, chosen to occupy a data cell in an unused corner of the computer-stored square image. By defining a region of interest around this cell, the resulting time-activity curve displays the physiological variable in temporal synchrony with the radiotracer distribution. (author)

  3. Studying rotational dynamics with a smartphone—accelerometer versus gyroscope

    Braskén, Mats; Pörn, Ray

    2017-07-01

    The wide-spread availability of smartphones makes them a valuable addition to the measurement equipment of both the physics classroom and the instructional physics laboratory, encouraging an active interaction between measurements and modeling activities. Two useful sensors, available in most modern smartphones and tablets, are the 3-axis acceleration sensor and the 3-axis gyroscope. We explore the strengths and weaknesses of each type of sensor and use them to study the rotational dynamics of objects rotating about a fixed axis. Care has to be taken when interpreting acceleration sensor data, and in some cases the gyroscope will allow for rotational measurements not easily replicated using the acceleration sensor.

  4. Dynamical study of a polydisperse hard-sphere system

    Nogawa, Tomoaki

    2010-08-10

    We study the interplay between the fluid-crystal transition and the glass transition of elastic sphere system with polydispersity using nonequilibrium molecular dynamics simulations. It is found that the end point of the crystal-fluid transition line, which corresponds to the critical polydispersity above which the crystal state is unstable, is on the glass transition line. This means that crystal and fluid states at the melting point becomes less distinguishable as polydispersity increases and finally they become identical state, i.e., marginal glass state, at critical polydispersity. © 2010 The American Physical Society.

  5. A study of dynamical behavior of space environment

    Wu, S. T.

    1974-01-01

    Studies have covered a wide range of problems in the space environment, such as the problems of the dynamical behavior of the thermosphere, hydromagnetic wave propagation in the ionosphere, and interplanetary space environment. The theories used to analyze these problems range from a continuum theory of magnetohydrodynamics to the kinetic theory of free molecular flow. This is because the problems encountered covered the entire range of the Knudsen number (i.e., the ratio of mean free path to the characteristic length). Significant results are summarized.

  6. Transverse flow reactor studies of the dynamics of radical reactions

    Macdonald, R.G. [Argonne National Laboratory, IL (United States)

    1993-12-01

    Radical reactions are in important in combustion chemistry; however, little state-specific information is available for these reactions. A new apparatus has been constructed to measure the dynamics of radical reactions. The unique feature of this apparatus is a transverse flow reactor in which an atom or radical of known concentration will be produced by pulsed laser photolysis of an appropriate precursor molecule. The time dependence of individual quantum states or products and/or reactants will be followed by rapid infrared laser absorption spectroscopy. The reaction H + O{sub 2} {yields} OH + O will be studied.

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

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

    2014-01-01

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

  8. Dynamic study of DSA by video-densitometry

    Imamura, Keiko; Tsukamoto, Hiroshi; Ashida, Hiroshi; Ishikawa, Tohru; Fujii, Masamichi; Uji, Teruyuki

    1985-01-01

    A system was developed for the dynamic study of DSA by video-densitometric technique. As subtraction images are stored to VTR in our DSA examinations, a frame counter was designed to select images on VTR at an arbitrary interval. ROI setting and video-densitometry were performed using a TV image processor and its host computer. Images were sampled at the rate of 3 frames per second, and clear time-density curves were obtained from brain DSA examinations. Although it takes about 30 minutes to analyse one examination, it is also possible to analyse previous data stored on VTR. For DSA systems having no additional digital storage unit, this method will be helpful. Reduction in image quality through VTR storage had no problem in video-densitometry. Phantom studies have been made concerning the temporal variation of the image brightness during the 20 second-exposure and also the effect of the subjects thickness on the contrast. Filtering for low-grade averaging is preferable for dynamic studies. (author)

  9. Mechanism and Regioselectivity of Rh(III)-Catalyzed Intermolecular Annulation of Aryl-Substituted Diazenecarboxylates and Alkenes: DFT Insights

    Ajitha, Manjaly John

    2016-02-05

    The mechanism of Rh-catalyzed intermolecular annulation of aryl-substituted diazenecarboxylates and alkenes was investigated using density functional theory (DFT) (PCM-M062X/6-311+G(d,p)//M062X/6-31G(d)). The acetate ligand (OAc)-assisted C-H activation via the formation of a five-membered rhodacycle (I-TS1; ΔG‡ = 19.4 kcal/mol) is more favorable compared to that via a four-membered intermediate (II-TS1; ΔG‡ = 27.8 kcal/mol). Our results also revealed that the seven-membered intermediate (I-3, ΔGrel = -6.8 kcal/mol) formed after the alkene insertion could undergo a coordination switch with the adjacent nitrogen atom (via TScs; ΔG‡ = 16.5 kcal/mol) to produce a thermodynamically stable six-membered intermediate (II-3, ΔGrel = -10.4 kcal/mol), eventually leading to a cyclization process followed by a barrierless ligand-assisted protonation to yield the final product. The β-hydride elimination product was found to be kinetically and thermodynamically undesirable. The rate-determining step is identified as the initial C-H activation, consistent with the previous kinetic studies. Notably, DFT studies offered important insights on the ability of the substrate (diazene carboxylate) to promote the switchable coordination site selectivity during the reaction to achieve a lower energy pathway. © 2016 American Chemical Society.

  10. Dynamics

    Goodman, Lawrence E

    2001-01-01

    Beginning text presents complete theoretical treatment of mechanical model systems and deals with technological applications. Topics include introduction to calculus of vectors, particle motion, dynamics of particle systems and plane rigid bodies, technical applications in plane motions, theory of mechanical vibrations, and more. Exercises and answers appear in each chapter.

  11. Noncovalent Intermolecular Interactions in Organic Electronic Materials: Implications for the Molecular Packing vs Electronic Properties of Acenes

    Sutton, Christopher

    2015-10-30

    Noncovalent intermolecular interactions, which can be tuned through the toolbox of synthetic chemistry, determine not only the molecular packing but also the resulting electronic, optical, and mechanical properties of materials derived from π-conjugated molecules, oligomers, and polymers. Here, we provide an overview of the theoretical underpinnings of noncovalent intermolecular interactions and briefly discuss the computational chemistry approaches used to understand the magnitude of these interactions. These methodologies are then exploited to illustrate how noncovalent intermolecular interactions impact important electronic properties-such as the electronic coupling between adjacent molecules, a key parameter for charge-carrier transport-through a comparison between the prototype organic semiconductor pentacene with a series of N-substituted heteropentacenes. Incorporating an understanding of these interactions into the design of organic semiconductors can assist in developing novel materials systems from this fascinating molecular class. © 2015 American Chemical Society.

  12. Semiconductor Nonlinear Dynamics Study by Broadband Terahertz Spectroscopy

    Ho, I.-Chen

    Semiconductor nonlinearity in the terahertz (THz) frequency range has been attracting considerable attention due to the recent development of high-power semiconductor-based nanodevices. However, the underlying physics concerning carrier dynamics in the presence of high-field THz transients is still obscure. This thesis introduces an ultrafast, time-resolved THz pump/THz probe approach to the study of semiconductor properties in the nonlinear regime. The carrier dynamics regarding two mechanisms, intervalley scattering and impact ionization, is observed for doped InAs on a sub-picosecond time scale. In addition, polaron modulation driven by intense THz pulses is experimentally and theoretically investigated. The observed polaron dynamics verifies the interaction between energetic electrons and a phonon field. In contrast to previous work which reports optical phonon responses, acoustic phonon modulations are addressed in this study. A further understanding of the intense field interacting with solid materials will accelerate the development of semiconductor devices. This thesis starts with the design and performance of a table-top THz spectrometer which has the advantages of ultra-broad bandwidth (one order higher bandwidth compared to a conventional ZnTe sensor) and high electric field strength (>100 kV/cm). Unlike the conventional THz time-domain spectroscopy, the spectrometer integrates a novel THz air-biased-coherent-detection (THz-ABCD) technique and utilizes selected gases as THz emitters and sensors. In comparison with commonly used electro-optic (EO) crystals or photoconductive (PC) dipole antennas, the gases have the benefits of no phonon absorption as existing in EO crystals and no carrier life time limitation as observed in PC dipole antennas. The newly development THz-ABCD spectrometer with a strong THz field strength capability provides a platform for various research topics especially on the nonlinear carrier dynamics of semiconductors. Two mechanisms

  13. Experimental study on dynamic buckling phenomena for supercavitating underwater vehicle

    Minho Chung

    2012-09-01

    Full Text Available Dynamic buckling, also known as parametric resonance, is one of the dynamic instability phenomena which may lead to catastrophic failure of structures. It occurs when compressive dynamic loading is applied to the structures. Therefore it is essential to establish a reliable procedure to test and evaluate the dynamic buckling behaviors of structures, especially when the structure is designed to be utilized in compressive dynamic loading environment, such as supercavitating underwater vehicle. In the line of thought, a dynamic buckling test system is designed in this work. Using the test system, dynamic buckling tests including beam, plate, and stiffened plate are carried out, and the dynamic buckling characteristics of considered structures are investigated experimentally as well as theoretically and numerically.

  14. Physical characteristics of cometary dust from dynamical studies - A review

    Sekanina, Z.

    1980-01-01

    Progress made in the determination of the physical characteristics of cometary dust particles from studies of dust tail dynamics is reviewed. Applications of the combined dynamical photometric approach of Finson and Probstein (1968) to studies of cometary tails exhibiting continuous light intensity variations are discussed, with attention given to determinations of the particle-size-related distribution function of the solar radiation pressure exerted on the particles, the contribution of comets to the interplanetary dust, calculations of dust ejection rates and a Monte Carlo approach to the analysis of dust tails. Investigations of dust streamers and striae, which are believed to be related to comet outbursts entailing brief but sharp enhancements of dust production, are then reviewed, with particular attention given to observations of Comet West 1976 VI. Finally, the question of cometary particle type is addressed, and it is pointed out that the presence of submicron absorbing particles in the striae of Comet West is not incompatible with the presence of micron-size dielectric particles in the inner coma.

  15. Individual renal function study using dynamic computed tomography

    Fukuda, Yutaka; Kiya, Keiichi; Suzuki, Yoshiharu

    1990-01-01

    Dynamic CT scans of individual kindneys were obtained after an intravenous bolus injection of contrast agent. Time-density curves measured from the renal cortex, medulla and pelvis revealed the changes in density produced by the contrast agent reflecting the differential phase of renal function. Renal cortical density increased rapidly after bolus administration and then renal medullary and pelvic density increased continuously. In analyzing time-density curve, the cortico-medullary junction time, which is the time when the cortical and medullary curves cross was 57±8 seconds in patients with normal renal function. The cortico-medullary junction time was delayed in patient with decreased glomerular filtration rate. The cortico-pelvic junction time, which is the time when the cortical and pelvic curves cross was 104±33 seconds in patients with normal renal function. The cortico-pelvic junction time was delayed in patients with declined urinary concentrating capacity. In patients with unilateral renal agenesis and patients who were treated surgically by ureteral sprits, the relationship between individual renal functions and these junction times was examined. As a result of study there were inversely significant correlations between C-M junction time and unilateral GFR and between C-P junction time and urinary concentrating capacity. These studies indicate that dynamic CT scanning is an effective way that individual renal function can be monitored and evaluated. (author)

  16. Dynamic Studies of Lung Fluid Clearance with Phase Contrast Imaging

    Kitchen, Marcus J.; Williams, Ivan; Irvine, Sarah C.; Morgan, Michael J.; Paganin, David M.; Lewis, Rob A.; Pavlov, Konstantin; Hooper, Stuart B.; Wallace, Megan J.; Siu, Karen K. W.; Yagi, Naoto; Uesugi, Kentaro

    2007-01-01

    Clearance of liquid from the airways at birth is a poorly understood process, partly due to the difficulties of observing and measuring the distribution of air within the lung. Imaging dynamic processes within the lung in vivo with high contrast and spatial resolution is therefore a major challenge. However, phase contrast X-ray imaging is able to exploit inhaled air as a contrast agent, rendering the lungs of small animals visible due to the large changes in the refractive index at air/tissue interfaces. In concert with the high spatial resolution afforded by X-ray imaging systems (<100 μm), propagation-based phase contrast imaging is ideal for studying lung development. To this end we have utilized intense, monochromatic synchrotron radiation, together with a fast readout CCD camera, to study fluid clearance from the lungs of rabbit pups at birth. Local rates of fluid clearance have been measured from the dynamic sequences using a single image phase retrieval algorithm

  17. Novel NMR tools to study structure and dynamics of biomembranes.

    Gawrisch, Klaus; Eldho, Nadukkudy V; Polozov, Ivan V

    2002-06-01

    Nuclear magnetic resonance (NMR) studies on biomembranes have benefited greatly from introduction of magic angle spinning (MAS) NMR techniques. Improvements in MAS probe technology, combined with the higher magnetic field strength of modern instruments, enables almost liquid-like resolution of lipid resonances. The cross-relaxation rates measured by nuclear Overhauser enhancement spectroscopy (NOESY) provide new insights into conformation and dynamics of lipids with atomic-scale resolution. The data reflect the tremendous motional disorder in the lipid matrix. Transfer of magnetization by spin diffusion along the proton network of lipids is of secondary relevance, even at a long NOESY mixing time of 300 ms. MAS experiments with re-coupling of anisotropic interactions, like the 13C-(1)H dipolar couplings, benefit from the excellent resolution of 13C shifts that enables assignment of the couplings to specific carbon atoms. The traditional 2H NMR experiments on deuterated lipids have higher sensitivity when conducted on oriented samples at higher magnetic field strength. A very large number of NMR parameters from lipid bilayers is now accessible, providing information about conformation and dynamics for every lipid segment. The NMR methods have the sensitivity and resolution to study lipid-protein interaction, lateral lipid organization, and the location of solvents and drugs in the lipid matrix.

  18. Intra- versus Intermolecular Hydrogen Bonding: Solvent-Dependent Conformational Preferences of a Common Supramolecular Binding Motif from 1 H NMR and Vibrational Circular Dichroism Spectra.

    Demarque, Daniel P; Merten, Christian

    2017-12-19

    When predicting binding properties of small molecules or larger supramolecular aggregates, intra- and intermolecular hydrogen bonds are often considered the most important factor. Spectroscopic techniques such as 1 H NMR spectroscopy are typically utilized to characterize such binding events, but interpretation is often qualitative and follows chemical intuition. In this study, we compare the effects of intramolecular hydrogen bonding and solvation on two chiral 2,6-pyridinediyl-dialkylamides. In comparison with 1 H NMR spectroscopy, vibrational circular dichroism (VCD) spectroscopy proved to be more sensitive to conformational changes. In fact, the change of the solvent from CDCl 3 to [D 6 ]DMSO generates mirror-image VCD spectra for the same enantiomer. Here, the common sense that the sterically less hindered group is more prone to solvation proved to be wrong according predicted VCD spectra, which clearly show that both asymmetric amide hydrogens are equally likely to be solvated, but never simultaneously. The competition between intra- and intermolecular hydrogen bonding and their importance for a correct prediction of spectral properties are discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Overtone vibrational spectroscopy in H2-H2O complexes: a combined high level theoretical ab initio, dynamical and experimental study.

    Ziemkiewicz, Michael P; Pluetzer, Christian; Nesbitt, David J; Scribano, Yohann; Faure, Alexandre; van der Avoird, Ad

    2012-08-28

    First results are reported on overtone (v(OH) = 2 ← 0) spectroscopy of weakly bound H(2)-H(2)O complexes in a slit supersonic jet, based on a novel combination of (i) vibrationally mediated predissociation of H(2)-H(2)O, followed by (ii) UV photodissociation of the resulting H(2)O, and (iii) UV laser induced fluorescence on the nascent OH radical. In addition, intermolecular dynamical calculations are performed in full 5D on the recent ab initio intermolecular potential of Valiron et al. [J. Chem. Phys. 129, 134306 (2008)] in order to further elucidate the identity of the infrared transitions detected. Excellent agreement is achieved between experimental and theoretical spectral predictions for the most strongly bound van der Waals complex consisting of ortho (I = 1) H(2) and ortho (I = 1) H(2)O (oH(2)-oH(2)O). Specifically, two distinct bands are seen in the oH(2)-oH(2)O spectrum, corresponding to internal rotor states in the upper vibrational manifold of Σ and Π rotational character. However, none of the three other possible nuclear spin modifications (pH(2)-oH(2)O, pH(2)-pH(2)O, or oH(2)-pH(2)O) are observed above current signal to noise level, which for the pH(2) complexes is argued to arise from displacement by oH(2) in the expansion mixture to preferentially form the more strongly bound species. Direct measurement of oH(2)-oH(2)O vibrational predissociation in the time domain reveals lifetimes of 15(2) ns and <5(2) ns for the Σ and Π states, respectively. Theoretical calculations permit the results to be interpreted in terms of near resonant energy levels and intermolecular alignment of the H(2) and H(2)O wavefunctions, providing insight into predissociation dynamical pathways from these metastable levels.

  20. Medial tibial pain: a dynamic contrast-enhanced MRI study.

    Mattila, K T; Komu, M E; Dahlström, S; Koskinen, S K; Heikkilä, J

    1999-09-01

    The purpose of this study was to compare the sensitivity of different magnetic resonance imaging (MRI) sequences to depict periosteal edema in patients with medial tibial pain. Additionally, we evaluated the ability of dynamic contrast-enhanced imaging (DCES) to depict possible temporal alterations in muscular perfusion within compartments of the leg. Fifteen patients with medial tibial pain were examined with MRI. T1-, T2-weighted, proton density axial images and dynamic and static phase post-contrast images were compared in ability to depict periosteal edema. STIR was used in seven cases to depict bone marrow edema. Images were analyzed to detect signs of compartment edema. Region-of-interest measurements in compartments were performed during DCES and compared with controls. In detecting periosteal edema, post-contrast T1-weighted images were better than spin echo T2-weighted and proton density images or STIR images, but STIR depicted the bone marrow edema best. DCES best demonstrated the gradually enhancing periostitis. Four subjects with severe periosteal edema had visually detectable pathologic enhancement during DCES in the deep posterior compartment of the leg. Percentage enhancement in the deep posterior compartment of the leg was greater in patients than in controls. The fast enhancement phase in the deep posterior compartment began slightly slower in patients than in controls, but it continued longer. We believe that periosteal edema in bone stress reaction can cause impairment of venous flow in the deep posterior compartment. MRI can depict both these conditions. In patients with medial tibial pain, MR imaging protocol should include axial STIR images (to depict bone pathology) with T1-weighted axial pre and post-contrast images, and dynamic contrast enhanced imaging to show periosteal edema and abnormal contrast enhancement within a compartment.

  1. Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics.

    Zecha, Jana; Meng, Chen; Zolg, Daniel Paul; Samaras, Patroklos; Wilhelm, Mathias; Kuster, Bernhard

    2018-05-01

    The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass spectrometry-based technologies allow determination of endogenous protein turnover on a proteome-wide scale. However, standard dynamic SILAC (Stable Isotope Labeling in Cell Culture) approaches can suffer from missing data across pulse time-points limiting the accuracy of such analysis. This issue is of particular relevance when studying protein stability at the level of proteoforms because often only single peptides distinguish between different protein products of the same gene. To address this shortcoming, we evaluated the merits of combining dynamic SILAC and tandem mass tag (TMT)-labeling of ten pulse time-points in a single experiment. Although the comparison to the standard dynamic SILAC method showed a high concordance of protein turnover rates, the pulsed SILAC-TMT approach yielded more comprehensive data (6000 proteins on average) without missing values. Replicate analysis further established that the same reproducibility of turnover rate determination can be obtained for peptides and proteins facilitating proteoform resolved investigation of protein stability. We provide several examples of differentially turned over splice variants and show that post-translational modifications can affect cellular protein half-lives. For example, N-terminally processed peptides exhibited both faster and slower turnover behavior compared with other peptides of the same protein. In addition, the suspected proteolytic processing of the fusion protein FAU was substantiated by measuring vastly different stabilities of the cleavage products. Furthermore, differential peptide turnover suggested a previously unknown mechanism of activity regulation by post-translational destabilization of cathepsin D as well as the DNA helicase BLM. Finally, our comprehensive data set facilitated a detailed evaluation of the impact of protein

  2. A general approach to intermolecular carbonylation of arene C-H bonds to ketones through catalytic aroyl triflate formation

    Garrison Kinney, R.; Tjutrins, Jevgenijs; Torres, Gerardo M.; Liu, Nina Jiabao; Kulkarni, Omkar; Arndtsen, Bruce A.

    2018-02-01

    The development of metal-catalysed methods to functionalize inert C-H bonds has become a dominant research theme in the past decade as an approach to efficient synthesis. However, the incorporation of carbon monoxide into such reactions to form valuable ketones has to date proved a challenge, despite its potential as a straightforward and green alternative to Friedel-Crafts reactions. Here we describe a new approach to palladium-catalysed C-H bond functionalization in which carbon monoxide is used to drive the generation of high-energy electrophiles. This offers a method to couple the useful features of metal-catalysed C-H functionalization (stable and available reagents) and electrophilic acylations (broad scope and selectivity), and synthesize ketones simply from aryl iodides, CO and arenes. Notably, the reaction proceeds in an intermolecular fashion, without directing groups and at very low palladium-catalyst loadings. Mechanistic studies show that the reaction proceeds through the catalytic build-up of potent aroyl triflate electrophiles.

  3. Nuclear magnetic resonance studies of macroscopic morphology and dynamics

    Barrall, G.A.; Lawrence Berkeley Lab., CA

    1995-09-01

    Nuclear magnetic resonance techniques are traditionally used to study molecular level structure and dynamics with a noted exception in medically applied NMR imaging (MRI). In this work, new experimental methods and theory are presented relevant to the study of macroscopic morphology and dynamics using NMR field gradient techniques and solid state two-dimensional exchange NMR. The goal in this work is not to take some particular system and study it in great detail, rather it is to show the utility of a number of new and novel techniques using ideal systems primarily as a proof of principle. By taking advantage of the analogy between NMR imaging and diffraction, one may simplify the experiments necessary for characterizing the statistical properties of the sample morphology. For a sample composed of many small features, e.g. a porous medium, the NMR diffraction techniques take advantage of both the narrow spatial range and spatial isotropy of the sample's density autocorrelation function to obtain high resolution structural information in considerably less time than that required by conventional NMR imaging approaches. The time savings of the technique indicates that NMR diffraction is capable of finer spatial resolution than conventional NMR imaging techniques. Radio frequency NMR imaging with a coaxial resonator represents the first use of cylindrically symmetric field gradients in imaging. The apparatus as built has achieved resolution at the micron level for water samples, and has the potential to be very useful in the imaging of circularly symmetric systems. The study of displacement probability densities in flow through a random porous medium has revealed the presence of features related to the interconnectedness of the void volumes. The pulsed gradient techniques used have proven successful at measuring flow properties for time and length scales considerably shorter than those studied by more conventional techniques

  4. Dynamic nuclear polarization of membrane proteins: covalently bound spin-labels at protein–protein interfaces

    Wylie, Benjamin J.; Dzikovski, Boris G.; Pawsey, Shane; Caporini, Marc; Rosay, Melanie; Freed, Jack H.; McDermott, Ann E.

    2015-01-01

    We demonstrate that dynamic nuclear polarization of membrane proteins in lipid bilayers may be achieved using a novel polarizing agent: pairs of spin labels covalently bound to a protein of interest interacting at an intermolecular interaction surface. For gramicidin A, nitroxide tags attached to the N-terminal intermolecular interface region become proximal only when bimolecular channels forms in the membrane. We obtained signal enhancements of sixfold for the dimeric protein. The enhancement effect was comparable to that of a doubly tagged sample of gramicidin C, with intramolecular spin pairs. This approach could be a powerful and selective means for signal enhancement in membrane proteins, and for recognizing intermolecular interfaces

  5. Theoretical study of ultraviolet induced photodissociation dynamics of sulfuric acid

    Murakami, Tatsuhiro; Ohta, Ayumi; Suzuki, Tomoya; Ikeda, Kumiko [Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-Cho, Chiyoda-ku, Tokyo 102-8554 (Japan); Danielache, Sebastian O. [Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-Cho, Chiyoda-ku, Tokyo 102-8554 (Japan); Earth-Life Science Institute (ELSI), Tokyo Institute of Technology (Japan); Department of Environmental Science and Techonology, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yoohama 226-8502 (Japan); Nanbu, Shinkoh, E-mail: shinkoh.nanbu@sophia.ac.jp [Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-Cho, Chiyoda-ku, Tokyo 102-8554 (Japan)

    2015-05-01

    Highlights: • Photodissociation dynamics of H{sub 2}SO{sub 4} at low-lying electronically excited states were investigated. • Photochemical processes were simulated by on-the-fly ab initio MD. • Sulfuric acid after the excitation to the S{sub 1} state dissociated to HSO{sub 4}(1{sup 2}A″) + H({sup 2}S). • Sulfuric acid after the excitation to the S{sub 2} state dissociated to HSO{sub 4}(2{sup 2}A″) + H({sup 2}S). • The energy region of the UV spectra where NMD fractionation may occur is predicted. - Abstract: Photodissociation dynamics of sulfuric acid after excitation to the first and second excited states (S{sub 1} and S{sub 2}) were studied by an on-the-fly ab initio molecular dynamics simulations based on the Zhu–Nakamura version of the trajectory surface hopping (ZN-TSH). Forces acting on the nuclear motion were computed on-the-fly by CASSCF method with Dunning’s augmented cc-pVDZ basis set. It was newly found that the parent molecule dissociated into two reaction-channels (i) HSO{sub 4}(1{sup 2}A″) + H({sup 2}S) by S{sub 1}-excitation, and (ii) HSO{sub 4}(2{sup 2}A″) + H({sup 2}S) by S{sub 2}-excitation. The direct dissociation dynamics yield products different from the SO{sub 2} + 2OH fragments often presented in the literature. Both channels result in the same product and differs only in the electronic state of the HSO{sub 4} fragment{sub .} The trajectories running on S{sub 2} do not hop with S{sub 0} and a nonadiabatic transition happens at the S{sub 2}–S{sub 1} conical intersection located at a longer OH bond-length than the S{sub 1}–S{sub 0} intersection producing an electronic excited state (2{sup 2}A″) of HSO{sub 4} product.

  6. NATO Advanced Study Institute on Nonequilibrium Phonon Dynamics

    1985-01-01

    Phonons are always present in the solid state even at an absolute temperature of 0 K where zero point vibrations still abound. Moreover, phonons interact with all other excitations of the solid state and, thereby, influence most of its properties. Historically experimental information on phonon transport came from measurements of thermal conductivity. Over the past two decades much more, and much more detailed, information on phonon transport and on many of the inherent phonon interaction processes have come to light from experiments which use nonequilibrium phonons to study their dynamics. The resultant research field has most recently blossomed with the development of ever more sophisticated experimental and theoretical methods which can be applied to it. In fact, the field is moving so rapidly that new members of the research community have difficulties in keeping up to date. This NATO Advanced Study Institute (ASI) was organized with the objective of overcoming the information barrier between those expert...

  7. Crossed molecular beam studies of unimolecular reaction dynamics

    Buss, R.J.

    1979-04-01

    The study of seven radical-molecule reactions using the crossed molecular beam technique with supersonic nozzle beams is reported. Product angular and velocity distributions were obtained and compared with statistical calculations in order to identify dynamical features of the reactions. In the reaction of chlorine and fluorine atoms with vinyl bromide, the product energy distributions are found to deviate from predictions of the statistical model. A similar effect is observed in the reaction of chlorine atoms with 1, 2 and 3-bromopropene. The reaction of oxygen atoms with ICl and CF 3 I has been used to obtain an improved value of the IO bond energy, 55.0 +- 2.0 kcal mol -1 . In all reactions studied, the product energy and angular distributions are found to be coupled, and this is attributed to a kinematic effect of the conservation of angular momentum

  8. Crossed-beam studies of the dynamics of radical reactions

    Liu, K. [Argonne National Laboratory, IL (United States)

    1993-12-01

    The objective of this program is to characterize the detailed dynamics of elementary radical reactions and to provide a better understanding of radical reactivity in general. The radical beam is typically generated by a laser photolysis method. After colliding with the reacting molecule in a crossed-beam apparatus, the reaction product state distribution is interrogated by laser spectroscopic techniques. Several radicals of combustion significance, such as O, CH, OH, CN and NCO have been successfully generated and their collisional behavior at the state-to-state integral cross section level of detail has been studied in this manner. During the past year, the detection system has been converted from LIF to REMPI schemes, and the emphasis of this program shifted to investigate the product angular distributions. Both inelastic and reactive processes have been studied.

  9. A Molecular Dynamics Study on Selective Cation Depletion from an Ionic Liquid Droplet under an Electric Field

    Yang, Yudong; Ahn, Myungmo; Im, Dojin; Oh, Jungmin; Kang, Inseok

    2017-11-01

    General electrohydrodynamic behavior of ionic liquid droplets under an electric field is investigated using MD simulations. Especially, a unique behavior of ion depletion of an ionic liquid droplet under a uniform electric field is studied. Shape deformation due to electric stress and ion distributions inside the droplet are calculated to understand the ionic motion of imidazolium-based ionic liquid droplets with 200 ion pairs of 2 kinds of ionic liquids: EMIM-NTf2 and EMIM-ES. The intermolecular force between cations and anions can be significantly different due to the nature of the structure and charge distribution of the ions. Together with an analytical interpretation of the conducting droplet in an electric field, the MD simulation successfully explains the mechanism of selective ion depletion of an ionic liquid droplet in an electric field. The selective ion depletion phenomenon has been adopted to explain the experimentally observed retreating motion of a droplet in a uniform electric field. The effect of anions on the cation depletion phenomenon can be accounted for from a direct approach to the intermolecular interaction. This research was supproted by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP) (No. 2017R1D1A1B05035211).

  10. Study of mass consciousnessand its dynamics in sociologic research

    S. V. Khobta

    2017-01-01

    Full Text Available The article is dedicated to analysis of the approaches used to study mass consciousness and the methods of their dynamics research. The two following approaches are reviewed: aggregative and group. The author shows that the study of the dynamics of mass consciousness in the modern day science is performed via computer modeling applying agent-oriented models and mass surveys of public opinion. Special attention is given to the concept of mass consciousness according to B. Grushin, where the mass consciousness is analyzed as a complex phenomenon according to its structure and the formation process. It is further analyzed what this particular concept is able to provide for the mass consciousness studies in the times of crises, similar to the situation of the military conflict at the East. It is then proven that the dialectic approach should be used as the basis for the mass consciousness studies adjusted for the interaction dynamics between the individual and collective, spontaneous and the institutionalized inside the collective consciousness. The mass consciousness is a complex structural formation, both heterogeneous and syncretical. Inside this structure one must distinguish between the layers that differ in depth and mobility and pay attention to its various conditions. The layers represent different worldviews, where, depending on the situation, scientific, religious or mystical images of the world can be actualized along with their ideological, moral and aesthetic precepts. These can cross, merge or coexist without contradicting each other and get actualized to a different extent. Besides the aforementioned the mass consciousness serves as a carrier of different kinds of deep, hard to change formations, such as «historical/collective memory», memlexes as well as superficial, most actualized forms, such as mems. It has «public/formal», socially accepted, and «private/real» levels that manifest themselves, in particular, in the forms of

  11. A study of dynamic foot pressure measurement in diabetic patients

    Milka D Madhale

    2017-01-01

    Full Text Available Introduction: Diabetic foot ulcer is a major source of morbidity and a leading cause of hospitalization. It is estimated that approximately 20% of hospital admissions among patients with diabetes mellitus are due to diabetic foot ulcer. It can lead to infection, gangrene, amputation, and even death if appropriate care is not provided. Overall, the lower limb amputation in diabetic patients is 15 times higher than in non-diabetics. In the majority of cases, the cause for the foot ulcer is the altered architecture of the foot due to neuropathy resulting in abnormal pressure points on the soles. Purpose: The aim of this study is to develop low cost, lightweight foot pressure scanner and check its reliability and validity which can help to prevent foot ulceration. Design/Methodology/Approach: In the present study, a low cost, lightweight foot pressure scanner is developed, and dynamic plantar pressures in a group of 110 Indian patients with diabetes with or without neuropathy and foot ulcers are measured. Practical Implications: If these pressure points can be detected, ulcers can be prevented by providing offloading footwear. Originality/Value: Differences are found in dynamic foot pressures in different study groups, namely, diabetic patients, patients with diabetic peripheral neuropathy, patients with foot ulcers, and nondiabetics. The differences are significant (P < 0.01, which showed the validity of the tool. Reliability and consistency of the tool was checked by test–retest method. Paper Type: Original Research work. Conclusion: Based on the results of the present study, it is concluded that the scanner is successfully developed and it can measure foot pressures. It is a novel device to proactively monitor foot health in diabetics in an effort to prevent and reduce diabetic foot complications.

  12. Study of nuclear statics and dynamics using the Wigner transform

    Shlomo, S.

    1983-01-01

    The Wigner phase-space distribution function, given as the shifted Fourier transform of the density matrix, provides a framework for an exact reformulation of non-relativistic quantum mechanics in terms of classical concepts. The Wigner distribution function (WDF), f(r-vector, p-vector), is considered as a quantum mechanical generalization of the classical phase space distribution function. While basic observables, such as matter density and momentum density, are given by the same integrals over f(r-vector, p-vector) as in classical physics, f(r-vector, p-vector) differs from its classical analog by the fact that it can assume negative values in some regions. However, it is known that the WDF is a useful and convenient tool for the study of the static and the dynamical aspects of many-body quantum systems, and the equation of motion for f(r-vector, p-vector) serves as a starting point for semi-classical approximations. The aim of this talk is to present and discuss some recent results for static and dynamic properties of nuclei obtained by exact evaluation of the WDF

  13. A parametric study of the dynamic failure of energetic composites

    Tanasoiu, Bogdan; Koslowski, Marisol

    2017-09-01

    Heating by frictional sliding of cracks is often considered to be one of the most important causes of localized melting and ignition in solid explosives. Furthermore, recent high speed X-ray phase contrast experiments on energetic composites under dynamic compression [Parab et al., Appl. Phys. Lett. 109(13) (2016)] show that most fracture events appear inside the particles. Initial cracks develop in regions where particles are close, and widespread fragmentation is observed in the interior of the particles as the stress waves propagate through the sample. However, most simulations have focused on interface debonding of energetic composites and, in general, do not include fracture of the particles explicitly. A phase field damage approach is used to model the dynamic response of a system of cyclotetramethylene-tetranitramine particles embedded in a Sylgard matrix. The simulations show several damage mechanisms observed in the experiments. The effects of the energy release rate and the initial crack distribution on the energy dissipation due to fracture are studied. The numerical results confirm that initial cracks play an important role in the evolution of damage, energy dissipation and consequently, the formation of hot-spots.

  14. Stability of nanofluids: Molecular dynamic approach and experimental study

    Farzaneh, H.; Behzadmehr, A.; Yaghoubi, M.; Samimi, A.; Sarvari, S.M.H.

    2016-01-01

    Highlights: • Nanofluid stability is investigated and discussed. • A molecular dynamic approach, considering different forces on the nanoparticles, is adopted. • Stability diagrams are presented for different thermo-fluid conditions. • An experimental investigation is carried out to confirm the theoretical approach. - Abstract: Nanofluids as volumetric absorbent in solar energy conversion devices or as working fluid in different heat exchangers have been proposed by various researchers. However, dispersion stability of nanofluids is an important issue that must be well addressed before any industrial applications. Conditions such as severe temperature gradient, high temperature of heat transfer fluid, nanoparticle mean diameters and types of nanoparticles and base fluid are among the most effective parameters on the stability of nanofluid. A molecular dynamic approach, considering kinetic energy of nanoparticles and DLVO potential energy between nanoparticles, is adopted to study the nanofluid stability for different nanofluids at different working conditions. Different forces such as Brownian, thermophoresis, drag and DLVO are considered to introduce the stability diagrams. The latter presents the conditions for which a nanofluid can be stable. In addition an experimental investigation is carried out to find a stable nanofluid and to show the validity of the theoretical approach. There is a good agreement between the experimental and theoretical results that confirms the validity of our theoretical approach.

  15. MD2036: UFO Dynamics Studies and UFO Fast Detection

    Belanger, Philippe; Valette, Matthieu; Lindstrom, Bjorn Hans Filip; Grob, Laura Katharina; Schmidt, Rudiger; Wollmann, Daniel

    2017-01-01

    UFOs are one of the remaining unknown related to LHC operation. Therefore, improving the understanding of UFO dynamics and validating the developed models against direct beam measurements is of fundamental importance in view of LHC operation at 7 TeV and with HL-LHC beam intensities. If not understood, UFOs could also be a showstopper for future machines such as FCC. This MD demonstrates new methods to study the dynamic behaviour of a calibrated UFO, simulated by the interaction of wire scanners with the beam. The events created during the MD were monitored using diamond BLMs in IR7, providing bunch-by-bunch resolution measurements. The analysis presented herein shows that blown-up bunches can be used to identify the plane of movement of UFOs, that bunch profiles and bunch sizes can be measured with dBLMs with good precision, that simulation of expected losses are in good agreement with measurements for oscillating bunches and that the space resolution of the acquisition system used during the MD is about 10 ...

  16. A study of tachyon dynamics for broad classes of potentials

    Quiros, Israel [Division de Ciencias e Ingenieria de la Universidad de Guanajuato, AP 150, 37150, Leon, Guanajuato (Mexico); Gonzalez, Tame [Departamento de Fisica, Universidad Central de Las Villas, 54830 Santa Clara (Cuba); Gonzalez, Dania; Napoles, Yunelsy [Departamento de Matematica, Universidad Central de Las Villas, 54830 Santa Clara (Cuba); GarcIa-Salcedo, Ricardo [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada-Legaria del IPN, Mexico DF (Mexico); Moreno, Claudia, E-mail: iquiros@Fisica.ugto.m, E-mail: tame@uclv.edu.c, E-mail: dgm@uclv.edu.c, E-mail: yna@uclv.edu.c, E-mail: rigarcias@ipn.m, E-mail: claudia.moreno@cucei.udg.m [Departamento de Fisica y Matematicas, Centro Universitario de Ciencias Exactas e IngenierIas, Av. Revolucion 1500 SR, Universidad de Guadalajara, 44430 Guadalajara, Jalisco (Mexico)

    2010-11-07

    We investigate in detail the asymptotic properties of tachyon cosmology for a broad class of self-interaction potentials. The present approach relies on an appropriate re-definition of the tachyon field, which, in conjunction with a method formerly applied in the bibliography in a different context allows us to generalize the dynamical systems study of tachyon cosmology to a wider class of self-interaction potentials beyond the (inverse) square-law one. It is revealed that independent of the functional form of the potential, the matter-dominated solution and the ultra-relativistic (also matter-dominated) solution are always associated with equilibrium points in the phase space of the tachyon models. The latter is always the past attractor, while the former is a saddle critical point. For inverse power-law potentials V{proportional_to}{phi}{sup -2{lambda}} the late-time attractor is always the de Sitter solution, while for sinh-like potentials V{proportional_to}sinh {sup -{alpha}}({lambda}{sup {phi}}), depending on the region of parameter space, the late-time attractor can be either the inflationary tachyon-dominated solution or the matter-scaling (also inflationary) phase. In general, for most part of known quintessential potentials, the late-time dynamics will be associated either with de Sitter inflation, or with matter-scaling, or with scalar field-dominated solutions.

  17. Hydrogen bond dynamics governs the effective photoprotection mechanism of plant phenolic sunscreens.

    Liu, Fang; Du, Likai; Lan, Zhenggang; Gao, Jun

    2017-02-15

    Sinapic acid derivatives are important sunscreen species in natural plants, which could provide protection from solar UV radiation. Using a combination of ultrafast excited state dynamics, together with classical molecular dynamics studies, we demonstrate that there is direct coupling of hydrogen bond motion with excited state photoprotection dynamics as part of the basic mechanism in solution. Beyond the intra-molecular degree of freedom, the inter-molecular motions on all timescales are potentially important for the photochemical or photophysical events, ranging from the ultrafast hydrogen bond motion to solvent rearrangements. This provides not only an enhanced understanding of the anomalous experimental spectroscopic results, but also the key idea in the development of sunscreen agents with improved photo-chemical properties. We suggest that the hydrogen bond dynamics coupled excited state photoprotection mechanism may also be possible in a broad range of bio-related molecules in the condensed phase.

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

    Dou, Wei-Dong [Department of Physics, Shaoxing University, Shaoxing 312000 (China); Center of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Material Science, City University of Hong Kong, Hong Kong (China); Huang, Shu-Ping [Department of Chemistry, University of South Dakota, Vermillion, South Dakota 57069 (United States); Lee, Chun-Sing, E-mail: apcslee@cityu.edu.hk [Center of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Material Science, City University of Hong Kong, Hong Kong (China)

    2015-10-07

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

  19. Identification of intra- and intermolecular disulfide bridges in the multidrug resistance transporter ABCG2

    Henriksen, Ulla Birk; Fog, Jacob U; Litman, Thomas

    2005-01-01

    cysteines predicted to be on the extracellular face of ABCG2. Upon mutation of Cys-592 or Cys-608 to alanine (C592A and C608A), ABCG2 migrated as a dimer in SDS-PAGE under non-reducing conditions; however, mutation of Cys-603 to Ala (C603A) caused the transporter to migrate as a single monomeric band....... Despite this change, C603A displayed efficient membrane targeting and preserved transport function. Because the transporter migrated as a dimer in SDS-PAGE, when only Cys-603 was present (C592A-C608A), the data suggest that Cys-603 forms a symmetrical intermolecular disulfide bridge in the ABCG2 homodimer...

  20. Influence of pressure on the crystallization of systems characterized by different intermolecular attraction

    Koperwas, K.; Affouard, F.; Gerges, J.; Valdes, L.-C.; Adrjanowicz, K.; Paluch, M.

    2017-12-01

    In this paper, we examine, in terms of the classical nucleation theory, how the strengthening of the attractive intermolecular interactions influences the crystallization process for systems like Lennard-Jones at different isobaric conditions. For this purpose, we modify the standard Lennard-Jones potential, and as a result, we obtain three different systems characterized by various strengths of attractive potentials occurring between molecules, which are in direct relationship to the physical quantities describing molecules, e.g., its polarizability or dipole moment. Based on performed analysis, we demonstrate that the molecular attraction primarily impacts the thermodynamics of the interface between liquid and crystal. This is reflected in the behavior of nucleation and overall crystallization rates during compression of the system.

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

    Hanni, Matti; Lantto, Perttu; Ilias, Miroslav

    2007-01-01

    Relativistic effects on the 129Xe nuclear magnetic resonance shielding and 131Xe 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 d, the anisotropy of the shielding tensor ?s, and the NQC constant along the internuclear axis ?ll are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full...... is obtained for d and ?s 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...

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

    Karayel, A.; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

    2015-01-01

    The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule

  3. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide.

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

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.

  4. Non-linear optical studies of adsorbates: Spectroscopy and dynamics

    Zhu, Xiangdong.

    1989-08-01

    In the first part of this thesis, we have established a systematic procedure to apply the surface optical second-harmonic generation (SHG) technique to study surface dynamics of adsorbates. In particular, we have developed a novel technique for studies of molecular surface diffusions. In this technique, the laser-induced desorption with two interfering laser beams is used to produce a monolayer grating of adsorbates. The monolayer grating is detected with diffractions of optical SHG. By monitoring the first-order second-harmonic diffraction, we can follow the time evolution of the grating modulation from which we are able to deduce the diffusion constant of the adsorbates on the surface. We have successfully applied this technique to investigate the surface diffusion of CO on Ni(111). The unique advantages of this novel technique will enable us to readily study anisotropy of a surface diffusion with variable grating orientation, and to investigate diffusion processes of a large dynamic range with variable grating spacings. In the second part of this work, we demonstrate that optical infrared-visible sum-frequency generation (SFG) from surfaces can be used as a viable surface vibrational spectroscopic technique. We have successfully recorded the first vibrational spectrum of a monolayer of adsorbates using optical infrared-visible SFG. The qualitative and quantitative correlation of optical SFG with infrared absorption and Raman scattering spectroscopies are examined and experimentally demonstrated. We have further investigated the possibility to use transient infrared-visible SFG to probe vibrational transients and ultrafast relaxations on surfaces. 146 refs

  5. Non-linear optical studies of adsorbates: Spectroscopy and dynamics

    Zhu, Xiangdong.

    1989-08-01

    In the first part of this thesis, we have established a systematic procedure to apply the surface optical second-harmonic generation (SHG) technique to study surface dynamics of adsorbates. In particular, we have developed a novel technique for studies of molecular surface diffusions. In this technique, the laser-induced desorption with two interfering laser beams is used to produce a monolayer grating of adsorbates. The monolayer grating is detected with diffractions of optical SHG. By monitoring the first-order second-harmonic diffraction, we can follow the time evolution of the grating modulation from which we are able to deduce the diffusion constant of the adsorbates on the surface. We have successfully applied this technique to investigate the surface diffusion of CO on Ni(111). The unique advantages of this novel technique will enable us to readily study anisotropy of a surface diffusion with variable grating orientation, and to investigate diffusion processes of a large dynamic range with variable grating spacings. In the second part of this work, we demonstrate that optical infrared-visible sum-frequency generation (SFG) from surfaces can be used as a viable surface vibrational spectroscopic technique. We have successfully recorded the first vibrational spectrum of a monolayer of adsorbates using optical infrared-visible SFG. The qualitative and quantitative correlation of optical SFG with infrared absorption and Raman scattering spectroscopies are examined and experimentally demonstrated. We have further investigated the possibility to use transient infrared-visible SFG to probe vibrational transients and ultrafast relaxations on surfaces. 146 refs.

  6. Dynamic radioisotopic study of the salivary glands. Quantification test

    Estour, A.-B.

    1976-01-01

    Quantified dynamic radioisotopic exploration, a new and rational examination, should find its place in a thorough check-up of the salivary glands together with clinical, immunological, anatomopathological and sialographic investigations. The object of this work was to standardise the test procedure with a view to routine use on patients and to define certain quantified parameters representing objectively the different aspects of the salivary functions. Our procedure through reeding sophisticated equipment, is simple to perform and relies on use of: radiotechnetium employed at activities which allow repetitive exlorations whereby pathological changes may be followed; the gamma camera and its data processing system which records all radioactive information obtained on the patient's head. These results will supply the data needed to judge the salivary functions as a whole. The apparatus used provides a remarkable pictorial record made up not only of morphological and functional images at each stage of the examination but also of ciphered radioactivity versus time curves for each of the main salivary glands and for any other zone of interest. From these curves it is then possible to define quantified parameters, reproducible and expressing functional activity. This procedure, safe and painless, seems to suit the patients who lie still without complaint for 60 minutes, 45 minutes for the concentration study and 15 minutes for the post-stimulus excretion study. The dynamic radioisotopic examination of the salivary glands, by the comparison of concentration and excretion images and by the study of parameters, separately and as a whole, is thus a useful complement to other paraclinical examinations and contributes essential information in most salivary diseases [fr

  7. Importance of the Donor:Fullerene intermolecular arrangement for high-efficiency organic photovoltaics

    Graham, Kenneth; Cabanetos, Clement; Jahnke, Justin P.; Idso, Matthew N.; El Labban, Abdulrahman; Ngongang Ndjawa, Guy Olivier; Heumueller, Thomas; Vandewal, Koen; Salleo, Alberto; Chmelka, Bradley F.; Amassian, Aram; Beaujuge, Pierre; McGehee, Michael D.

    2014-01-01

    The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b]dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) 13C{1H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems

  8. Importance of the Donor:Fullerene intermolecular arrangement for high-efficiency organic photovoltaics

    Graham, Kenneth

    2014-07-09

    The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b]dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) 13C{1H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems

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

    Christensen, Anders S., E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Cui, Qiang, E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu [Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706 (United States); Elstner, Marcus [Theoretische Chemische Biologie, Universität Karlsruhe, Kaiserstr. 12, 76131 Karlsruhe (Germany)

    2015-08-28

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

  10. Dynamic Studies with Radioisotopes in Medicine. Proceedings of the Symposium on Dynamics Studies with Radioisotopes in Clinical Medicine and Research

    1971-01-01

    Observations on the temporal patterns of uptake, metabolism, clearance or excretion of administered radioactive materials form the basis of many important applications of radioisotopes in clinical medicine and research. Such applications include studies of organ function, of regional blood flow and of the turnover of various substances in the human body. Newly available radioisotopes, new instruments such as gamma came ras, new techniques and new methods of data analysis based on the use of analogue and digital computers are continually enlarging the scope of the applications. Progress in these matters was discussed at the Symposium on Dynamic Studies with Radioisotopes in Clinical Medicine and Research, organized by the lnternational Atomic Energy Agency and held in Rotterdam, The Netherlands, from 31 August to 4 September 1970. A total of 315 participants nominated by 39 countries and 4 international organizations attended, and the 70 papers presented cove r the theoretical aspects of dynamic studies, the development of techniques and instruments for such studies, and specific applications in studies of thyroid, renal, hepatic and splenic function, mineral metabolism, regional blood flow, and cardiac and pulmonary function. The proceedings include the full texts of all the papers presented together with the edited discussions. Invited review papers deal with the general aspects of the various main groups of applications covered. Many of the applications described have already reached the stage of routine use; others are still in the developmental stage. Of particular note in the latter connection are applications based on the quantitative analysis of scintillation camera data. The many papers presented on these topics and the ensuing discussions indicate the great interest now shown in this promising area of development. It is hoped that the proceedings will provide a valuable guide to the present status of the subject

  11. A molecular dynamics study of helium bombardments on tungsten nanoparticles

    Li, Min; Hou, Qing; Cui, Jiechao; Wang, Jun

    2018-06-01

    Molecular dynamics simulations were conducted to study the bombardment process of a single helium atom on a tungsten nanoparticle. Helium atoms ranging from 50 eV to 50 keV were injected into tungsten nanoparticles with a diameter in the range of 2-12 nm. The retention and reflection of projectiles and sputtering of nanoparticles were calculated at various times. The results were found to be relative to the nanoparticle size and projectile energy. The projectile energy of 100 eV contributes to the largest retention of helium atoms in tungsten nanoparticles. The most obvious difference in reflection exists in the range of 3-10 keV. Around 66% of sputtering atoms is in forward direction for projectiles with incident energy higher than 10 keV. Moreover, the axial direction of the nanoparticles was demonstrated to influence the bombardment to some degree.

  12. A microstructural study of dynamic crack propagation in nuclear graphites

    Burchell, T.D.; McEnaney, B.; Tucker, M.O.; Rose, A.P.G.

    1986-01-01

    This paper reports a new microstructural study of dynamic crack propagation in three nuclear graphites: (i) PGA, the moderator material in UK Magnox reactors; (ii) IMl-24, the moderator material in UK Advanced gas cooled reactors (AGR); and (iii) a pitch coke graphite, which is used in the fabrication of AGR fuel sleeves. The fracture mechanisms in nuclear graphites are initiated by microcrack formation at low stresses. Typically, microcracks form in regions of well-aligned binder or at favourably-oriented pores, where stress is concentrated. With increasing applied loads, microcracks propagate taking advantage of easy cleavage paths or linking with pores. Eventually, coalescence of such cracks and inherent porosity produces a crack of critical length for fast fracture. (orig./MM)

  13. Dynamic stall study of a multi-element airfoil

    Tung, Chee; Mcalister, Kenneth W.; Wang, Clin M.

    1992-01-01

    Unsteady flow behavior and load characteristics of a VR-7 airfoil with and without a slat were studied in the water tunnel of the Aeroflightdynamics Directorate, NASA Ames Research Center. Both airfoils were oscillated sinusoidally between 5 and 25 degrees at a Reynolds number of 200,000 to obtain the unsteady lift, drag and pitching moment data. A fluorescing dye was released from an orifice located at the leading edge of the airfoil for the purpose of visualizing the boundary layer and wake flow. The flow field and load predictions of an incompressible Navier-Stokes code based on a velocity-vorticity formulation were compared with the test data. The test and predictions both confirm that the slatted VR-7 airfoil delays both static and dynamic stall as compared to the VR-7 airfoil alone.

  14. Experimental Study and Dynamic Modeling of Metal Rubber Isolating Bearing

    Zhang, Ke; Zhou, Yanguo; Jiang, Jian

    2015-01-01

    In this paper, dynamic shear mechanical properties of a new metal rubber isolating bearing is tested and studied. The mixed damping model is provided for theoretical modeling of MR isolating bearing, the shear stiffness and damping characteristics of the MR bearing can be analyzed separately and easily discussed, and the mixed damping model is proved to be an rather effective approach. The test results indicate that loading frequency bears little impact over shear property of metal rubber isolating bearing, the total energy consumption of metal rubber isolating bearing increases with the increase in loading amplitude. With the increase in loading amplitude, the stiffness of the isolating bearing will reduce showing its “soft property”; and the type of damping force gradually changes to be close to dry friction. The features of “soft property” and dry friction energy consumption of metal rubber isolating bearing are very useful in practical engineering application. (paper)

  15. A cluster dynamics study of fission gases in uranium dioxide

    Skorek, Richard

    2013-01-01

    During in-pile irradiation of nuclear fuels a lot of rare gases are produced, mainly xenon and krypton. The behaviour of these highly insoluble fission gases may lead to an additional load of the cladding, which may have detrimental safety consequences. For these reasons, fission gas behaviour (diffusion and clustering) has been extensively studied for years.In this work, we present an application of Cluster Dynamics to address the behaviour of fission gases in UO_2 which simultaneously describes changes in rare gas atom and point defect concentrations in addition to the bubble size distribution. This technique, applied to Kr implanted and annealed samples, yields a precise interpretation of the release curves and helps justifying the estimation of the Kr diffusion coefficient, which is a data very difficult to obtain due to the insolubility of the gas. (author) [fr

  16. Studies on population dynamic of diamondback moth in the field

    Malakrong, A.; Limohpasmanee, W.; Keawchoung, P.; Kodcharint, P.

    1994-01-01

    The population dynamic of diamondback moth larva in the field was studied at Khao Khor High-land Agricultural Research Station during August-October 1993 and February-April 1994. The distribution patterns of diamondback moth larva was clumped when population was low and would change to be random when population was high. The maximun and minimum number of diamondback moth in the field were 71,203 and 2,732 larva/rai during March and September. Temperature, rainfall and age of cabbage were slightly relative with number of larva (r=-0.2891, p=0.30; r=-0.2816, p=0.31 and r=0.2931, p=0.29 respectively) but relative humidity has no effect on number of larva

  17. Study of Dynamic Characteristics of Slow-Changing Process

    Yinong Li

    2000-01-01

    Full Text Available A vibration system with slow-changing parameters is a typical nonlinear system. Such systems often occur in the working and controlled process of some intelligent structures when vibration and deformation exist synchronously. In this paper, a system with slow-changing stiffness, damping and mass is analyzed in an intelligent structure. The relationship between the amplitude and the frequency of the system is studied, and its dynamic characteristic is also discussed. Finally, a piecewise linear method is developed on the basis of the asymptotic method. The simulation and the experiment show that a suitable slow-changing stiffness can restrain the amplitude of the system when the system passes through the resonant region.

  18. Study on Dynamic Alignment Technology of COIL Resonator

    Xiong, M D; Zou, X J; Guo, J H; Jia, S N; Zhang, Z B

    2006-01-01

    The performance of great power chemical oxygen-iodine laser (COIL) beam is decided mostly by resonator mirror maladjustment and environment vibration. To improve the performance of light beam, an auto-alignment device is used in COIL resonator, the device can keep COIL resonator collimating by adjusting the optical components of resonator. So the coupling model of COIL resonator is present. The multivariable self study fuzzy uncoupling arithmetic and six-dimensional micro drive technology are used to design a six-input-three-output uncoupling controller, resulting in the realization of the high precision dynamic alignment. The experiments indicate that the collimating range of this system is 8 mrad, precision is 5 urad and frequency response is 20Hz, which meet the demand of resonator alignment system

  19. Size optimization and dynamics studies for a heliac stellarators reactor

    Perez-Navarro, A.; Fraguas, A.L.; Ochando, M.A.; Garcia Gonzalo, L.

    1995-01-01

    Design studies for a stellarator reactor based on a heliac configuration have been addressed to determine the minimum size requirements and operational techniques for plasma start-up and run-down. Assuming constraints derived from the available technologies and plasma parameter limitations, a device with a major radius of 15 m and a plasma radius of 2 m is obtained, for a magnetic field of 5 T and a power output around 1 GW(e). A coil system with enough space for blanket and shielding has been defined. Finally it is proved that by a continuous use of a modest amount of auxiliary power, all dynamical process of the plant operation can be eased. 13 refs

  20. Molecular dynamics study of shock compression in porous silica glass

    Jones, Keith; Lane, J. Matthew D.; Vogler, Tracy J.

    2017-06-01

    The shock response of porous amorphous silica is investigated using classical molecular dynamics, over a range of porosity ranging from fully dense (2.21 g/cc) down to 0.14 g/cc. We observe an enhanced densification in the Hugoniot response at initial porosities above 50 %, and the effect increases with increasing porosity. In the lowest initial densities, after an initial compression response, the systems expand with increased pressure. These results show good agreement with experiments. Mechanisms leading to enhanced densification will be explored, which appear to differ from mechanisms observed in similar studies in silicon. Sandia National Laboratories is a multi mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  1. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  2. On the representation of the electric charge distribution in ethane for calculations of the molecular quadrupole moment and intermolecular electrostatic energy

    Hansen, Flemming Yssing; Alldredge, G. P.; Bruch, L. W.

    1985-01-01

    and gives a repulsive rather than an attractive electrostatic interaction at typical intermolecular distances. In the local multipole model, the atom-site dipoles give the largest contribution to both the molecular quadrupole moment and the intermolecular interaction. The Journal of Chemical Physics...

  3. Structure and Dynamics of Polymers in Cylindrical Nanoconfinement: A Molecular Dynamics Study

    Pressly, James; Riggleman, Robert; Winey, Karen

    The structure and dynamics of polymers under nanoconfinement is critical for understanding how polymers behave in applications from hydraulic fracking to fabricating integrated circuits. We previously used simulations to explore the effect of the diameter of cylindrical pores (d = 10-40 σ, where σ is the unit length in reduced units) on polymer end-to-end distance (Ree,perp, Ree,par) , entanglement density, melt diffusion coefficient (D), and local relaxation time (τperp, τpar) at fixed polymer chain length (N = 350). These studies found D, Ree,par, and τperp increased with increasing confinement while entanglement density, Ree,perp, and τpar decreased. Experiments also found that D increased but to a lesser extent. Here, we examine the molecular weight dependence of these properties using N = 25, 50, 100, 200, 350, and 500 confined to pores of diameter 14 σ to examine a range of confinements. Our preliminary results show that as N increases D and Ree,par, increase as well, relative to the unconfined state, while entanglement density and Ree,perp decrease, consistent with our previous work. Interestingly, τ is shown to be independent of chain length indicating the impact of confinement imposed by reducing pore diameter is distinct from that imposed by increasing chain length.

  4. Calculation of dynamic and electronic properties of perfect and defect crystals by semiempirical quantum mechanical methods

    Zunger, A.

    1975-07-01

    Semiempirical all-valence-electron LCAO methods, that were previously used to study the electronic structure of molecules are applied to three problems in solid state physics: the electronic band structure of covalent crystals, point defect problems in solids and lattice dynamical study of molecular crystals. Calculation methods for the electronic band structure of regular solids are introduced and problems regarding the computation of the density matrix in solids are discussed. Three models for treating the electronic eigenvalue problem in the solid, within the proposed calculation schemes, are discussed and the proposed models and calculation schemes are applied to the calculation of the electronic structure of several solids belonging to different crystal types. The calculation models also describe electronic properties of deep defects in covalent insulating crystals. The possible usefulness of the semieipirical LCAO methods in determining the first order intermolecular interaction potential in solids and an improved model for treating the lattice dynamics and related thermodynamical properties of molecular solids are presented. The improved lattice dynamical is used to compute phonon dispersion curves, phonon density of states, stable unit cell structure, lattice heat capacity and thermal crystal parameters, in α and γ-N 2 crystals, using the N 2 -N 2 intermolecular interaction potential that has been computed from the semiempirical LCAO methods. (B.G.)

  5. Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET)

    Jensen, Anders A.; Hansen, Jakob L; Sheikh, Søren P

    2002-01-01

    -induced intermolecular movements in the CaR homodimer using the new bioluminescence resonance energy transfer technique, BRET2, which is based on the transference of energy from Renilla luciferase (Rluc) to the green fluorescent protein mutant GFP2. We tagged CaR with Rluc and GFP2 at different intracellular locations...

  6. Coiodação de alquenos com nucleófilos oxigenados: reações intermoleculares

    Sanseverino Antonio Manzolillo

    2001-01-01

    Full Text Available A review on the electrophilic addition of iodine to alkenes in the presence of oxygen containing nucleophiles (cohalogenation reaction is presented. The intermolecular reactions are discussed with emphasis in methods of reaction and synthetic applications of the resulting vicinal iodo-functionalized products (iodohydrins, beta-iodoethers and beta-iodocarboxylates.

  7. Intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization reactions of 1,6-enynes with symmetrical and unsymmetrical alkynes†

    Andrew Evans, P.; Sawyer, James R.; Lai, Kwong Wah; Huffman, John C.

    2006-01-01

    The crossed intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization of carbon and heteroatom tethered 1,6-enynes can be accomplished with symmetrical and unsymmetrical alkynes, to afford the corresponding bicyclohexadienes in an efficient and highly selective manner. PMID:16075089

  8. Synthesis of benzimidazoles by potassium tert-butoxide-promoted intermolecular cyclization reaction of 2-iodoanilines with nitriles.

    Xiang, Shi-Kai; Tan, Wen; Zhang, Dong-Xue; Tian, Xian-Li; Feng, Chun; Wang, Bi-Qin; Zhao, Ke-Qing; Hu, Ping; Yang, Hua

    2013-11-14

    The synthesis of benzimidazoles by intermolecular cyclization reaction of 2-iodoanilines with nitriles has been developed. These reactions proceeded without the aid of any transition metals or ligands and just using KOBu(t) as the base. A variety of substituted benzimidazole derivatives can be synthesized by the approach.

  9. Dynamic studies of nano-confined polymer thin films

    Geng, Kun

    Polymer thin films with the film thickness (h0 ) below 100 nm often exhibit physical properties different from the bulk counterparts. In order to make the best use of polymer thin films in applications, it is important to understand the physical origins of these deviations. In this dissertation, I will investigate how different factors influence dynamic properties of polymer thin films upon nano-confinement, including glass transition temperature (Tg), effective viscosity (etaeff) and self-diffusion coefficient (D ). The first part of this dissertation concerns the impacts of the molecular weight (MW) and tacticity on the Tg's of nano-confined polymer films. Previous experiments showed that the Tg of polymer films could be depressed or increased as h0 decreases. While these observations are usually attributed to the effects of the interfaces, some experiments suggested that MW's and tacticities might also play a role. To understand the effects of these factors, the Tg's of silica-based poly(alpha-methyl styrene) (PalphaMS/SiOx) and poly(methyl methacrylate) (PMMA/SiOx) thin films were studied, and the results suggested that MW's and tacticities influence Tg in nontrivial ways. The second part concerns an effort to resolve the long-standing controversy about the correlation between different dynamics of polymer thin films upon nano-confinement. Firstly, I discuss the experimental results of Tg, D and etaeff of poly(isobutyl methacrylate) films supported by silica (PiBMA/SiOx). Both T g and D were found to be independent of h 0, but etaeff decreased with decreasing h 0. Since both D and etaeff describe transport phenomena known to depend on the local friction coefficient or equivalently the local viscosity, it is questionable why D and etaeff displayed seemingly inconsistent h 0 dependencies. We envisage the different h0 dependencies to be caused by Tg, D and etaeff being different functions of the local T g's (Tg,i) or viscosities (eta i). By assuming a three

  10. Structural, Dynamic, and Vibrational Properties during Heat Transfer in Si/Ge Superlattices: A Car-Parrinello Molecular Dynamics Study

    Ji, Pengfei; Zhang, Yuwen; Yang, Mo

    2016-01-01

    The structural, dynamic, and vibrational properties during the heat transfer process in Si/Ge superlattices, are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) ar...

  11. Scilab software package for the study of dynamical systems

    Bordeianu, C. C.; Beşliu, C.; Jipa, Al.; Felea, D.; Grossu, I. V.

    2008-05-01

    This work presents a new software package for the study of chaotic flows and maps. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well known examples are implemented, with the capability of the users inserting their own ODE. Program summaryProgram title: Chaos Catalogue identifier: AEAP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 885 No. of bytes in distributed program, including test data, etc.: 5925 Distribution format: tar.gz Programming language: Scilab 3.1.1 Computer: PC-compatible running Scilab on MS Windows or Linux Operating system: Windows XP, Linux RAM: below 100 Megabytes Classification: 6.2 Nature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE). Solution method: Numerical solving of ordinary differential equations. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincaré sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies. Restrictions: The package routines are normally able to handle ODE systems of high orders (up to order twelve and possibly higher), depending on the nature of the problem. Running time: 10 to 20 seconds for problems that do not

  12. Rotational coherence spectroscopy at FLASH. Toward dynamic studies in nanosuperfluids

    Kickermann, Andreas

    2013-07-15

    The field of molecular physics, which is focusing on molecular motion in the transition states of physical, chemical, and biological changes, is a wide-spread research area. It strives to reveal the structural and functional properties of molecules, the chemical bonds between atoms and the time evolution. Many processes occurring in nature upon electronic excitation proceed on the ultrafast femtosecond timescale and can be triggered by modern ultrashort femtosecond-laser sources under laboratory conditions. In the present thesis pump-probe studies were performed to follow molecular motion using ultrashort light pulses in the nanometer wavelength range provided by an XUV freeelectron laser (FEL). In detail, alignment of molecular species in space under field-free conditions was investigated. In the specific case of rotational wave packets in molecules the rotational dynamics shows characteristic temporal features, which contain a wealth of information on molecular structure and give insight into molecular coupling mechanisms, i.e. rotational constants and transition frequencies. Within this thesis, Rotational Coherence Spectroscopy (RCS) reveals wave-packet motion observed by subsequent Coulomb explosion of Raman excited carbon monoxide, which results in a time-dependent asymmetry of spatial fragmentation patterns. With the method presented here, the time resolution to elucidate the fast dynamics of strong couplings can be pushed toward a single rotational period even for the fastest rotors. This is due to large pump-probe delays with small subpicosecond step size. This kind of spectroscopy can also be expanded to molecular species, which are not accessible by other powerful spectroscopic methods, such as Fourier-transform microwave spectroscopy (FTMW). Furthermore, it allows to measure weak molecular couplings on a long timescale (large pump-probe delays), e.g. couplings of molecules in a solution or molecules dissolved in quantum fluids. This is valuable to

  13. Rotational coherence spectroscopy at FLASH. Toward dynamic studies in nanosuperfluids

    Kickermann, Andreas

    2013-07-01

    The field of molecular physics, which is focusing on molecular motion in the transition states of physical, chemical, and biological changes, is a wide-spread research area. It strives to reveal the structural and functional properties of molecules, the chemical bonds between atoms and the time evolution. Many processes occurring in nature upon electronic excitation proceed on the ultrafast femtosecond timescale and can be triggered by modern ultrashort femtosecond-laser sources under laboratory conditions. In the present thesis pump-probe studies were performed to follow molecular motion using ultrashort light pulses in the nanometer wavelength range provided by an XUV freeelectron laser (FEL). In detail, alignment of molecular species in space under field-free conditions was investigated. In the specific case of rotational wave packets in molecules the rotational dynamics shows characteristic temporal features, which contain a wealth of information on molecular structure and give insight into molecular coupling mechanisms, i.e. rotational constants and transition frequencies. Within this thesis, Rotational Coherence Spectroscopy (RCS) reveals wave-packet motion observed by subsequent Coulomb explosion of Raman excited carbon monoxide, which results in a time-dependent asymmetry of spatial fragmentation patterns. With the method presented here, the time resolution to elucidate the fast dynamics of strong couplings can be pushed toward a single rotational period even for the fastest rotors. This is due to large pump-probe delays with small subpicosecond step size. This kind of spectroscopy can also be expanded to molecular species, which are not accessible by other powerful spectroscopic methods, such as Fourier-transform microwave spectroscopy (FTMW). Furthermore, it allows to measure weak molecular couplings on a long timescale (large pump-probe delays), e.g. couplings of molecules in a solution or molecules dissolved in quantum fluids. This is valuable to

  14. Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals

    Patriarca, M.; Kuronen, A.; Robles, M.; Kaski, K.

    2007-01-01

    The study of crystal defects and the complex processes underlying their formation and time evolution has motivated the development of the program ALINE for interactive molecular dynamics experiments. This program couples a molecular dynamics code to a Graphical User Interface and runs on a UNIX-X11 Window System platform with the MOTIF library, which is contained in many standard Linux releases. ALINE is written in C, thus giving the user the possibility to modify the source code, and, at the same time, provides an effective and user-friendly framework for numerical experiments, in which the main parameters can be interactively varied and the system visualized in various ways. We illustrate the main features of the program through some examples of detection and dynamical tracking of point-defects, linear defects, and planar defects, such as stacking faults in lattice-mismatched heterostructures. Program summaryTitle of program:ALINE Catalogue identifier:ADYJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYJ_v1_0 Program obtainable from: CPC Program Library, Queen University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers:DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers Installations:Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland Operating systems under which the program has been tested:True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4 Programming language used:Standard C and MOTIF libraries Memory required to execute with typical data:6 Mbytes but may be larger depending on the system size No. of lines in distributed program, including test data, etc.:16 901 No. of bytes in distributed program, including test data, etc.:449 559 Distribution format:tar.gz Nature of physical problem:Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are

  15. Classical and quantum molecular dynamics in NMR spectra

    Szymański, Sławomir

    2018-01-01

    The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

  16. Cellular Automata Models Applied to the Study of Landslide Dynamics

    Liucci, Luisa; Melelli, Laura; Suteanu, Cristian

    2015-04-01

    Landslides are caused by complex processes controlled by the interaction of numerous factors. Increasing efforts are being made to understand the spatial and temporal evolution of this phenomenon, and the use of remote sensing data is making significant contributions in improving forecast. This paper studies landslides seen as complex dynamic systems, in order to investigate their potential Self Organized Critical (SOC) behavior, and in particular, scale-invariant aspects of processes governing the spatial development of landslides and their temporal evolution, as well as the mechanisms involved in driving the system and keeping it in a critical state. For this purpose, we build Cellular Automata Models, which have been shown to be capable of reproducing the complexity of real world features using a small number of variables and simple rules, thus allowing for the reduction of the number of input parameters commonly used in the study of processes governing landslide evolution, such as those linked to the geomechanical properties of soils. This type of models has already been successfully applied in studying the dynamics of other natural hazards, such as earthquakes and forest fires. The basic structure of the model is composed of three modules: (i) An initialization module, which defines the topographic surface at time zero as a grid of square cells, each described by an altitude value; the surface is acquired from real Digital Elevation Models (DEMs). (ii) A transition function, which defines the rules used by the model to update the state of the system at each iteration. The rules use a stability criterion based on the slope angle and introduce a variable describing the weakening of the material over time, caused for example by rainfall. The weakening brings some sites of the system out of equilibrium thus causing the triggering of landslides, which propagate within the system through local interactions between neighboring cells. By using different rates of

  17. Microscopic studies of nonlocal spin dynamics and spin transport (invited)

    Adur, Rohan; Du, Chunhui; Cardellino, Jeremy; Scozzaro, Nicolas; Wolfe, Christopher S.; Wang, Hailong; Herman, Michael; Bhallamudi, Vidya P.; Pelekhov, Denis V.; Yang, Fengyuan; Hammel, P. Chris, E-mail: hammel@physics.osu.edu [Department of Physics, The Ohio State University, Columbus, Ohio 43210 (United States)

    2015-05-07

    Understanding the behavior of spins coupling across interfaces in the study of spin current generation and transport is a fundamental challenge that is important for spintronics applications. The transfer of spin angular momentum from a ferromagnet into an adjacent normal material as a consequence of the precession of the magnetization of the ferromagnet is a process known as spin pumping. We find that, in certain circumstances, the insertion of an intervening normal metal can enhance spin pumping between an excited ferromagnetic magnetization and a normal metal layer as a consequence of improved spin conductance matching. We have studied this using inverse spin Hall effect and enhanced damping measurements. Scanned probe magnetic resonance techniques are a complementary tool in this context offering high resolution magnetic resonance imaging, localized spin excitation, and direct measurement of spin lifetimes or damping. Localized magnetic resonance studies of size-dependent spin dynamics in the absence of lithographic confinement in both ferromagnets and paramagnets reveal the close relationship between spin transport and spin lifetime at microscopic length scales. Finally, detection of ferromagnetic resonance of a ferromagnetic film using the photoluminescence of nitrogen vacancy spins in neighboring nanodiamonds demonstrates long-range spin transport between insulating materials, indicating the complexity and generality of spin transport in diverse, spatially separated, material systems.

  18. Microscopic studies of nonlocal spin dynamics and spin transport (invited)

    Adur, Rohan; Du, Chunhui; Cardellino, Jeremy; Scozzaro, Nicolas; Wolfe, Christopher S.; Wang, Hailong; Herman, Michael; Bhallamudi, Vidya P.; Pelekhov, Denis V.; Yang, Fengyuan; Hammel, P. Chris

    2015-05-01

    Understanding the behavior of spins coupling across interfaces in the study of spin current generation and transport is a fundamental challenge that is important for spintronics applications. The transfer of spin angular momentum from a ferromagnet into an adjacent normal material as a consequence of the precession of the magnetization of the ferromagnet is a process known as spin pumping. We find that, in certain circumstances, the insertion of an intervening normal metal can enhance spin pumping between an excited ferromagnetic magnetization and a normal metal layer as a consequence of improved spin conductance matching. We have studied this using inverse spin Hall effect and enhanced damping measurements. Scanned probe magnetic resonance techniques are a complementary tool in this context offering high resolution magnetic resonance imaging, localized spin excitation, and direct measurement of spin lifetimes or damping. Localized magnetic resonance studies of size-dependent spin dynamics in the absence of lithographic confinement in both ferromagnets and paramagnets reveal the close relationship between spin transport and spin lifetime at microscopic length scales. Finally, detection of ferromagnetic resonance of a ferromagnetic film using the photoluminescence of nitrogen vacancy spins in neighboring nanodiamonds demonstrates long-range spin transport between insulating materials, indicating the complexity and generality of spin transport in diverse, spatially separated, material systems.

  19. Microscopic studies of nonlocal spin dynamics and spin transport (invited)

    Adur, Rohan; Du, Chunhui; Cardellino, Jeremy; Scozzaro, Nicolas; Wolfe, Christopher S.; Wang, Hailong; Herman, Michael; Bhallamudi, Vidya P.; Pelekhov, Denis V.; Yang, Fengyuan; Hammel, P. Chris

    2015-01-01

    Understanding the behavior of spins coupling across interfaces in the study of spin current generation and transport is a fundamental challenge that is important for spintronics applications. The transfer of spin angular momentum from a ferromagnet into an adjacent normal material as a consequence of the precession of the magnetization of the ferromagnet is a process known as spin pumping. We find that, in certain circumstances, the insertion of an intervening normal metal can enhance spin pumping between an excited ferromagnetic magnetization and a normal metal layer as a consequence of improved spin conductance matching. We have studied this using inverse spin Hall effect and enhanced damping measurements. Scanned probe magnetic resonance techniques are a complementary tool in this context offering high resolution magnetic resonance imaging, localized spin excitation, and direct measurement of spin lifetimes or damping. Localized magnetic resonance studies of size-dependent spin dynamics in the absence of lithographic confinement in both ferromagnets and paramagnets reveal the close relationship between spin transport and spin lifetime at microscopic length scales. Finally, detection of ferromagnetic resonance of a ferromagnetic film using the photoluminescence of nitrogen vacancy spins in neighboring nanodiamonds demonstrates long-range spin transport between insulating materials, indicating the complexity and generality of spin transport in diverse, spatially separated, material systems

  20. Computational fluid dynamics (CFD) studies of a miniaturized dissolution system.

    Frenning, G; Ahnfelt, E; Sjögren, E; Lennernäs, H

    2017-04-15

    Dissolution testing is an important tool that has applications ranging from fundamental studies of drug-release mechanisms to quality control of the final product. The rate of release of the drug from the delivery system is known to be affected by hydrodynamics. In this study we used computational fluid dynamics to simulate and investigate the hydrodynamics in a novel miniaturized dissolution method for parenteral formulations. The dissolution method is based on a rotating disc system and uses a rotating sample reservoir which is separated from the remaining dissolution medium by a nylon screen. Sample reservoirs of two sizes were investigated (SR6 and SR8) and the hydrodynamic studies were performed at rotation rates of 100, 200 and 400rpm. The overall fluid flow was similar for all investigated cases, with a lateral upward spiraling motion and central downward motion in the form of a vortex to and through the screen. The simulations indicated that the exchange of dissolution medium between the sample reservoir and the remaining release medium was rapid for typical screens, for which almost complete mixing would be expected to occur within less than one minute at 400rpm. The local hydrodynamic conditions in the sample reservoirs depended on their size; SR8 appeared to be relatively more affected than SR6 by the resistance to liquid flow resulting from the screen. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. DYNAMIC STRATEGIC-FIT DAN KINERJA: STUDI PADA PERBANKAN SYARIAH

    Sugiyarti F. Laela

    2014-06-01

    Full Text Available Although the growth of Islamic banking assets is still high, the market share of Islamic banking reached only ± 4,92% by the end of May 2014. Islamic banks should implement an appropriate strategy to face dynamic changes in the business environment. The education strategy is one of the business strategies of Islamic banks that remain a priority today. It provides information and understanding for society about the function, role, activities, and products as well as services of Islamic banks. This study examines the impact of fit between the education strategy and contingency variables (known as strategic-fit on performance. The contingency variables include efficiency of input, organizational competency, CEO tenure, and composition of shariah supervisory board. The performance of Islamic banks consists of both financial and social performances. Using the data from 1997 to 2012 of 10 fully-fledge Islamic banks in Indonesia and least squares method, this study shows that the efficiency of input has a positive effect on the educational strategy implementation. On the other hand, the composition of shariah supervisory board and organizational competency negatively affect the implementation of the educational strategy. Nevertheless, there is no strong evidence that CEO tenure influences the implementation of the educational strategy. Adopting the method of Van de Ven and Drazin (1985 to determine the degree of strategic misfit, this study finds that the misfit between educational strategy and its contingency variables has a negative effect on financial performance, but no significant effect of misfit on social performance.

  2. A perceptual study on dynamical form in music

    Hjortkjær, Jens; Nielbo, Frederik

    2010-01-01

    The concept of dynamical form is presented as a dimen- sion of music perception. Dynamical form refers to the subjective perception of temporal events in music (explo- sive, fading out, rising etc.). In a behavioral experiment listeners were asked to categorize musical excerpts vary- ing in music...

  3. Study of physical properties of the dynamic filter

    Souza, Roberto Salomon

    2004-02-01

    This paper presents a characterization of the physical properties of the dynamic filter of Clinac 2300 CD linear accelerator of Varian Medical Systems, installed at the Cancer National Institute (INCA), Rio de Janeiro. The 'dynamic filter factors' were measured for the 6 and 15 MV photons, in squared and rectangular fields, and compared with factors furnished at the accelerator manual and used by the planning system, IN and OUT positions, at the maximum dose depths, 5 cm, 10 cm and 29 cm, for the 6 and 15 MV photons energies. The results demonstrated that the 'dynamic filter factors' does not changes with depth and the PDP for the opened field are the same for the fields with dynamic filters. Last but not least the dynamic filters were measured and compared with the nominal angles of the accelerator and the planning system, where some discrepancies were reported

  4. Static structure, microscopic dynamics and electronic properties of the liquid Bi–Li alloy. An ab initio molecular dynamics study

    Souto, J; Alemany, M M G; Gallego, L J; González, L E; González, D J

    2013-01-01

    We report an ab initio molecular dynamics study of the static, dynamic and electronic properties of the liquid Bi x Li 1−x alloy, which is a complex binary system with a marked tendency to heterocoordination. The calculated total static structure factors are in good agreement with the available experimental data. The partial dynamic structure factors exhibit side peaks indicative of propagating density fluctuations, and for some concentrations we have found a density fluctuation mode with phase velocity greater than the hydrodynamic sound velocity. We have also evaluated other dynamical properties such as the diffusion coefficients, the shear viscosity and the adiabatic sound velocity. The electronic density of states show that the liquid Bi x Li 1−x alloy has a metallic character, although with strong deviations from the free-electron parabolic curve. The results reported improve the understanding of binary liquid alloys with both fast and slow propagating collective modes. (paper)

  5. Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

    Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

    2013-12-21

    The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

  6. Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

    Ji, Pengfei; Zhang, Yuwen; Yang, Mo

    2013-01-01

    The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective

  7. Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

    Ji, Pengfei; Zhang, Yuwen; Yang, Mo

    2013-12-01

    The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

  8. Incoherent scatter studies of upper atmosphere dynamics and coding technique

    Haeggstroem, Ingemar.

    1990-09-01

    Observations by the EISCAT incoherent scatter radar are used to study the dynamics of the auroral upper atmosphere. The study describes some effects of the strong plasma convection occurring at these latitudes and a new coding technique for incoherent scatter radars. A technique to determine the thermospheric neutral wind from incoherent scatter measurements is described. Simultaneous Fabry-Perot interferometer measurements of the wind are compared with those derived from the radar data. F-region electron density depletions in the afternoon/evening sector of the auroral zone, identified as the main ionospheric trough, are investigated. In a statistical study, based on wide latitude scanning experiment made at solar minimum, the trough appearance at a given latitude is compared to the geomagnetic index K p , and an empirical model predicting the latitude of the trough is proposed. Detailed studies, using different experiment modes, show that the equatorward edge of the auroral oval is co-located of up to 1 degree poleward of the trough minimum, which in turn is co-located with the peak convective electric field, with its boundary 1 degree - 2 degree equatorward of the trough minimum. It is shown that the F-region ion composition changes from pure 0 + to molecular ion dominated (NO + /O 2 + ) as the trough moves into the region probed by the radar. In a special case, where a geomagnetic sudden impulse caused an expansion of the plasma convection pattern, the equatorward trough progression is studied together with ionosonde measurements. A new coding technique for incoherent scatter radar measurement is introduced and described. The method, called alternating codes, provides significantly more accurate estimates of the plasma parameters than can be obtained by frequency commutated multipulse measurements. Simple explanations of the method are given as well as a precise definition. Two examples of application of the alternating codes are presented, showing the high

  9. Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions.

    Wen, Jin; Li, Wei; Chen, Shuang; Ma, Jing

    2016-08-17

    Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.

  10. Mechanical properties of irradiated nanowires – A molecular dynamics study

    Figueroa, Emilio [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla, 653 Santiago (Chile); Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente, Universidad Tecnológica Metropolitana, Santiago 7800002 (Chile); Tramontina, Diego [Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza (Argentina); Instituto de Bioingeniería, Universidad de Mendoza, 5500 Mendoza (Argentina); Gutiérrez, Gonzalo, E-mail: gonzalo@fisica.ciencias.uchile.cl [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla, 653 Santiago (Chile); Bringa, Eduardo [Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza (Argentina)

    2015-12-15

    In this work we study, by means of molecular dynamics simulation, the change in the mechanical properties of a gold nanowire with pre-existing radiation damage. The gold nanowire is used as a simple model for a nanofoam, made of connected nanowires. Radiation damage by keV ions leads to the formation of a stacking fault tetrahedron (SFT), and this defect leads to a reduced plastic threshold, as expected, when the nanowire is subjected to tension. We quantify dislocation and twin density during the deformation, and find that the early activation of the SFT as a dislocation source leads to reduced dislocation densities compared to the case without radiation damage. In addition, we observed a total destruction of the SFT, as opposed to a recent simulation study where it was postulated that SFTs might act as self-generating dislocation sources. The flow stress at large deformation is also found to be slightly larger for the irradiated case, in agreement with recent experiments. - Highlights: • Stacking Fault Tetrahedra (SFT) formation proceeds by cascades, containing typically a vacancy cluster and interstitials. • Applied tension leads to the destruction of the SFT, in contrast to a recently reported case of a SFT which soften the NW. • After the initial dislocation activity, strength is controlled by a few surviving dislocations.

  11. Molecular dynamics study of the vaporization of an ionic drop.

    Galamba, N

    2010-09-28

    The melting of a microcrystal in vacuum and subsequent vaporization of a drop of NaCl were studied through molecular dynamics simulations with the Born-Mayer-Huggins-Tosi-Fumi rigid-ion effective potential. The vaporization was studied for a single isochor at increasing temperatures until the drop completely vaporized, and gaseous NaCl formed. Examination of the vapor composition shows that the vapor of the ionic drop and gaseous NaCl are composed of neutral species, the most abundant of which, ranging from simple NaCl monomers (ion pairs) to nonlinear polymers, (Na(n)Cl(n))(n=2-4). The enthalpies of sublimation, vaporization, and dissociation of the different vapor species are found to be in reasonable agreement with available experimental data. The decrease of the enthalpy of vaporization of the vapor species, with the radius of the drop decrease, accounts for a larger fraction of trimers and tetramers than that inferred from experiments. Further, the rhombic dimer is significantly more abundant than its linear isomer although the latter increases with the temperature. The present results suggest that both trimers and linear dimers may be important to explain the vapor pressure of molten NaCl at temperatures above 1500 K.

  12. Study of a possible S=+1 dynamically generated baryonic resonance

    Sarkar, S.; Oset, E.; Vaca, M.J.V.

    2005-01-01

    Starting from the lowest-order chiral Lagrangian for the interaction of the baryon decuplet with the octet of pseudoscalar mesons we find an attractive interaction in the ΔK channel with L=0 and I=1, while the interaction is repulsive for I=2. The attractive interaction leads to a pole in the second Riemann sheet of the complex plane and manifests itself in a large strength of the K scattering amplitude close to the ΔK threshold, which is not the case for I=2. However, we also make a study of uncertainties in the model and conclude that the existence of this pole depends sensitively upon the input used and can disappear within reasonable variations of the input parameters. We take advantage to study the stability of the other poles obtained for the 3/2 - dynamically generated resonances of the model and conclude that they are stable and not contingent to reasonable changes in the input of the theory

  13. Molecular dynamics study of the vaporization of an ionic drop

    Galamba, N.

    2010-09-01

    The melting of a microcrystal in vacuum and subsequent vaporization of a drop of NaCl were studied through molecular dynamics simulations with the Born-Mayer-Huggins-Tosi-Fumi rigid-ion effective potential. The vaporization was studied for a single isochor at increasing temperatures until the drop completely vaporized, and gaseous NaCl formed. Examination of the vapor composition shows that the vapor of the ionic drop and gaseous NaCl are composed of neutral species, the most abundant of which, ranging from simple NaCl monomers (ion pairs) to nonlinear polymers, (NanCln)n=2-4. The enthalpies of sublimation, vaporization, and dissociation of the different vapor species are found to be in reasonable agreement with available experimental data. The decrease of the enthalpy of vaporization of the vapor species, with the radius of the drop decrease, accounts for a larger fraction of trimers and tetramers than that inferred from experiments. Further, the rhombic dimer is significantly more abundant than its linear isomer although the latter increases with the temperature. The present results suggest that both trimers and linear dimers may be important to explain the vapor pressure of molten NaCl at temperatures above 1500 K.

  14. Robophysical study of jumping dynamics on granular media

    Aguilar, Jeffrey; Goldman, Daniel I.

    2016-03-01

    Characterizing forces on deformable objects intruding into sand and soil requires understanding the solid- and fluid-like responses of such substrates and their effect on the state of the object. The most detailed studies of intrusion in dry granular media have revealed that interactions of fixed-shape objects during free impact (for example, cannonballs) and forced slow penetration can be described by hydrostatic- and hydrodynamic-like forces. Here we investigate a new class of granular interactions: rapid intrusions by objects that change shape (self-deform) through passive and active means. Systematic studies of a simple spring-mass robot jumping on dry granular media reveal that jumping performance is explained by an interplay of nonlinear frictional and hydrodynamic drag as well as induced added mass (unaccounted by traditional intrusion models) characterized by a rapidly solidified region of grains accelerated by the foot. A model incorporating these dynamics reveals that added mass degrades the performance of certain self-deformations owing to a shift in optimal timing during push-off. Our systematic robophysical experiment reveals both new soft-matter physics and principles for robotic self-deformation and control, which together provide principles of movement in deformable terrestrial environments.

  15. HOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDY OF MYCOBACTERIUM TUBERCULOSIS UREASE

    Lisnyak Yu. V.

    2017-10-01

    Full Text Available Introduction. M. tuberculosis urease (MTU is an attractive target for chemotherapeutic intervention in tuberculosis by designing new safe and efficient enzyme inhibitors. A prerequisite for designing such inhibitors is an understanding of urease's three-dimensional (3D structure organization. 3D structure of M. tuberculosis urease is unknown. When experimental three-dimensional structure of a protein is not known, homology modeling, the most commonly used computational structure prediction method, is the technique of choice. This paper aimed to build a 3D-structure of M. tuberculosis urease by homology modeling and to study its stability by molecular dynamics simulations. Materials and methods. To build MTU model, five high-resolution X-ray structures of bacterial ureases with three-subunit composition (2KAU, 5G4H, 4UBP, 4СEU, and 4EPB have been selected as templates. For each template five stochastic alignments were created and for each alignment, a three-dimensional model was built. Then, each model was energy minimized and the models were ranked by quality Z-score. The MTU model with highest quality estimation amongst 25 potential models was selected. To further improve structure quality the model was refined by short molecular dynamics simulation that resulted in 20 snapshots which were rated according to their energy and the quality Z-score. The best scoring model having minimum energy was chosen as a final homology model of 3D structure for M. tuberculosis. The final model of MTU was also validated by using PDBsum and QMEAN servers. These checks confirmed good quality of MTU homology model. Results and discussion. Homology model of MTU is a nonamer (homotrimer of heterotrimers, (αβγ3 consisting of 2349 residues. In MTU heterotrimer, sub-units α, β, and γ tightly interact with each other at a surface of approximately 3000 Å2. Sub-unit α contains the enzyme active site with two Ni atoms coordinated by amino acid residues His347, His

  16. Crystal structure and pair potentials: A molecular-dynamics study

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  17. Molecular dynamics of TBP and DBP studied by neutron transmission

    Salles Filho, J.B.V.; Refinetti, M.E.; Fulfaro, R.; Vinhas, L.A.

    1984-04-01

    Differences between the properties of TBP and DBP, concerning the uranium extraction processes, may be related to certain characteristics of the molecular dynamics of each compound. In order to investigate the dynamical behaviour of hydrogen in these molecules, neutron transmission of TBP and DBP has been measured as a function of neutron wavelenght in the range 4.0 - 6.0 A, at room temperature. Scattering cross sections per hydrogen atom have been obtained. From the comparison with results previously obtained for n-butanol, similar dynamical behaviour of butyl radicals in these compounds could be observed. This similarity indicates that the presence of two or three butyl radicals in butylphosphate molecules does not exert influence in the hydrogen motion of methyl and methylene groups. This suggests that the different chemical behaviour between TBP and DBP is related to the dynamics of the hydrogen directly bound to the DBP phosphate group.(Author) [pt

  18. Effect of donor orientation on ultrafast intermolecular electron transfer in coumarin-amine systems

    Singh, P. K.; Nath, S.; Bhasikuttan, A. C.; Kumbhakar, M.; Mohanty, J.; Sarkar, S. K.; Mukherjee, T.; Pal, H.

    2008-01-01

    Effect of donor amine orientation on nondiffusive ultrafast intermolecular electron transfer (ET) reactions in coumarin-amine systems has been investigated using femtosecond fluorescence upconversion measurements. Intermolecular ET from different aromatic and aliphatic amines used as donor solvents to the excited coumarin-151 (C151) acceptor occurs with ultrafast rates such that the shortest fluorescence lifetime component (τ 1 ) is the measure of the fastest ET rate (τ 1 =τ ET fast =(k ET fast ) -1 ), assigned to the C151-amine contact pairs in which amine donors are properly oriented with respect to C151 to maximize the acceptor-donor electronic coupling (V el ). It is interestingly observed that as the amine solvents are diluted by suitable diluents (either keeping solvent dielectric constant similar or with increasing dielectric constant), the τ 1 remains almost in the similar range as long as the amine dilution does not cross a certain critical limit, which in terms of the amine mole fraction (x A ) is found to be ∼0.4 for aromatic amines and ∼0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the τ 1 values are seen to increase very sharply. The large difference in the critical x A values involving aromatic and aliphatic amine donors has been rationalized in terms of the largely different orientational restrictions for the ET reactions as imposed by the aliphatic (n-type) and aromatic (π-type) nature of the amine donors [A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008)]. Since the highest occupied molecular orbital (HOMO) of the n-type aliphatic amines is mostly centralized at the amino nitrogen, only some specific orientations of these amines with respect to the close-contact acceptor dye [also of π-character; A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008) and E. W. Castner et al., J. Phys. Chem. A 104, 2869 (2000)] can give suitable V el and thus ultrafast ET reaction. In contrary, the

  19. Effects of Weak Intermolecular Interactions on the Molecular Isomerism of Tricobalt Metal Chains

    Poulsen, R.; Overgaard, J.; Schulman, A.; Stergaard, C.; Murillo, C.; Spackman, M.; Iversen, B.

    2009-01-01

    Depending on the number of interstitial solvent molecules, n, crystals of the linear chain compound Co3(dipyridylamide)4Cl2·nCH2Cl2 adopt either symmetrical or unsymmetrical metal chain structures. We explore here the possible reasons for such behavior using Hirshfeld surface analysis of intermolecular interactions as well as the charge density determined from 100(1) K X-ray diffraction data on the unsymmetrical complex Co3(dipyridylamide)4Cl2·2.11CH2Cl2, u-1, and crystal structures of u-1 determined from single crystal synchrotron X-ray diffraction data at 20, 150, and 300 K. The new crystal structures are compared with previous structural results on a crystal with slightly different solvent content. This change in solvent content only affects the bond distances to atom Co(3), which are also strongly affected by temperature changes due to a spin crossover transition. Large differences in intermolecular interactions are revealed by the Hirshfeld surface analysis between symmetrical (s-1) and unsymmetrical (u-1) crystal solvates, suggesting that the molecular isomerism is strongly influenced by crystal packing effects. Topological analysis of the static electron density of u-1 suggests that there is direct metal-metal bonding for both the shorter Co(1)-Co(2) and the longer Co(2)-Co(3) contact. The approximate description of the system as a (Co2)2+-dimer and an isolated Co2+-ion is reflected in the character of the metal-ligand interactions, which are more ionic for the isolated Co(3) atom, and the topological charges Co(1)+0.50, Co(2)+0.77, and Co(3)+1.36. The two termini of u-1 are found to be very different, both in terms of structural surroundings as well as topology. The central Co(2) atom is similar to a cobalt atom in a tetragonally distorted octahedral environment resulting in preferred occupancy in the t2g orbitals. The Co(1) atom has significant deformation in the xz and yz planes (z along the chain axis, x and y toward ligands) reflecting covalent

  20. Superheating of Ag nanowires studied by molecular dynamics simulations

    Duan Wenshi; Ling Guangkong; Hong Lin; Li Hong; Liang Minghe

    2008-01-01

    The melting process of Ag nanowires was studied by molecular dynamics (MD) simulations at the atomic level. It is indicated that the Ag nanowires with Ni coating can be superheated depending on their radius and size. Also, in this paper the mechanism of superheating was analyzed and ascribed to the epitaxial Ag/Ni interface suppressing the nucleation and growth of melt. For the analysis, a thermodynamic model was constructed to describe the superheating mechanism of the Ni-coated Ag nanowires by considering the Ag/Ni interface free energy. We showed that the nucleation and growth of the Ag melt phase are both suppressed by the low energy Ag/Ni interfaces in Ni-coated Ag wires and the suppression of melt growth is crucial and plays a major role in the process of melting. The thermodynamic analysis gave a quantitative relation of superheating with the Ag wire radius and the contact angle of melting. The superheating decreased with Ag wire radius and also depended on the Ag/Ni interfacial condition. The results of the thermodynamic model were consistent with those of the MD simulations

  1. Studying protein assembly with reversible Brownian dynamics of patchy particles

    Klein, Heinrich C. R.; Schwarz, Ulrich S.

    2014-01-01

    Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly

  2. Hydration of amino acids: FTIR spectra and molecular dynamics studies.

    Panuszko, Aneta; Adamczak, Beata; Czub, Jacek; Gojło, Emilia; Stangret, Janusz

    2015-11-01

    The hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results, molecular dynamics simulations of amino acids were performed. The structural-energetic characteristic of these solute-affected water molecules shows that, on average, water affected by amino acids forms stronger and shorter H-bonds than those in pure water. Differences in the influence of amino acids on water structure have been noticed. The effect of the hydrophobic side chain of an amino acid on the solvent interactions seems to be enhanced because of the specific cooperative coupling of water strong H-bond chain, connecting the carboxyl and amino groups, with the clathrate-like H-bond network surrounding the hydrocarbon side chain. The parameter derived from the spectral data, which corresponds to the contributions of the population of weak hydrogen bonds of water molecules which have been substituted by the stronger ones in the hydration sphere of amino acids, correlated well with the amino acid hydrophobicity indexes.

  3. Model Studies of the Dynamics of Bacterial Flagellar Motors

    Bai, F; Lo, C; Berry, R; Xing, J

    2009-03-19

    The Bacterial Flagellar Motor is a rotary molecular machine that rotates the helical filaments which propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation and switching mechanism of the motor. In our previous paper, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here we further analyze this model. In this paper we show (1) the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with the latest experiment by Lo et al.; (2) with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, recently observed by Yuan and Berg; (3) the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwelling time distribution. Predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental verification.

  4. Static and dynamic light scattering studies on dilute polyrotaxane solutions

    Kume, Tetsuya; Araki, Jun; Sakai, Yasuhiro; Mayumi, Koichi; Kidowaki, Masatoshi; Yokoyama, Hideaki; Ito, Kohzo

    2009-08-01

    Static and dynamic light scattering measurements were performed for dilute polyrotaxane solutions in different types of solvent systems, i.e. dimethylacetamide (DMAc) or dimethylformamide (DMF) containing 1-6 wt% lithium chloride (LiCl), 1 M aqueous sodium hydroxide (NaOH) and dimethylsulfoxide (DMSO). No aggregation of the polyrotaxane in DMF/LiCl was confirmed in the present study. Radius of gyration of the dissolved polyrotaxane was largest in NaOHaq., followed by values in amide solvents/LiCl and that in DMSO, and was probably dominated not by Coulombic repulsion but by the mutual affinity between solvent and polyrotaxane. Ratio of radius of gyration to hydrodynamic radius suggested the flexible random-coiled conformation in DMSO and relatively more extended, semi-flexible ones in amide solvents/LiCl and NaOHaq. The obtained values of second virial coefficient and weight average molecular weight seemed to be affected by a potential change in differential refractive index increments, caused by selective macrocationization or ionization.

  5. ESF collection effectiveness, a study in fine particle dynamics

    Winegardner, W.K.; Owczarski, P.C.

    1985-04-01

    The characterization and dynamic behavior of fine particles are the main subjects of an ongoing investigation of the particle collection effectiveness of the engineered safety feature (ESF) systems in nuclear power plants. This investigation is part of a larger study of the release of radionuclides to the environment from such plants during postulated accidents that are severe but extremely unlikely. The ESF systems are installed to prevent the occurrence of severe accidents or mitigate their consequences. Several of these engineered systems can serve as particle collection devices. This report focuses on the analytical models that were developed to predict particle behavior in two systems that were not specifically designed for particle retention: the ice compartments of ice condenser containment systems in Pressurized Water Reactors (PWRs) and the suppression pools of Boiling Water Reactors (BWRs). The following section summarizes the topics considered in the development of models and computer codes for estimating the particle retention effectiveness of these two ESF systems. After the summary this paper describes the two ESF systems in more detail and discusses the behavior of particles in both situations

  6. Morphological findings in dynamic swallowing studies of symptomatic patients

    Scharitzer, Martina; Pokieser, Peter; Schober, Ewald; Schima, Wolfgang; Eisenhuber, Edith; Stadler, Alfred; Memarsadeghi, Mazda; Partik, Bernhard; Lechner, Gerhard [Department of Radiology, University of Vienna (Austria); Ludwig Boltzmann Institute for Radiologic Tumor Diagnosis, Vienna (Austria); Ekberg, Olle [Department of Diagnostic Radiology, Malmoe University Hospital (Sweden)

    2002-05-01

    The aim of this study was to assess the role of videofluoroscopy in the detection of structural abnormalities of the pharynx and esophagus in patients with different symptoms of impaired deglutition. Dynamic radiographic recording of deglutition was performed in 3193 consecutive patients (1578 men, 1615 women; mean age 54 years) suffering from dysphagia, suspicion of aspiration, globus sensation, and non-cardiac chest pain. We assessed different structural lesions from the oral cavity to the esophagus and classified them into eight categories. Their frequency and association with the different clinical symptoms were evaluated. Videofluoroscopy revealed 1040 structural abnormalities in 833 patients (26%) including mass lesions from the oral cavity to hyoid/larynx (n=66), pharyngeal diverticula (n=181), pharyngeal masses (n=78), other pharyngeal narrowings (n=71), webs (n=98), masses (n=39), and other narrowings (n=73) of the upper esophageal sphincter, esophageal diverticula (n=80), esophageal webs, rings and strictures (n=194), and intrinsic and extrinsic esophageal lesions (n=160). There was a considerable variance of findings for different symptoms. In a large proportion of symptomatic patients videofluoroscopy detects morphological abnormalities along pharynx and esophagus often combined with functional disorders. This fact underlines the role of videofluoroscopy as a diagnostic test for function as well as morphology. (orig.)

  7. Molecular dynamics studies of radiation effects in silicon carbide

    Diaz de la Rubia, T.; Caturla, M.J.; Tobin, M.

    1995-01-01

    We discuss results of molecular dynamics computer simulation studies of 3 keV and 5 keV displacement cascades in β-SIC, and compare them to results of 5 keV cascades in pure silicon. The SiC simulations are performed with the Tersoff potential. For silicon we use the Stillinger-Weber potential. Simulations were carried out for Si recoils in 3 dimensional cubic computational cells With periodic boundary conditions and up to 175,616 atoms. The cascade lifetime in SiC is found to be extremely short. This, combined with the high melting temperature of SiC, precludes direct lattice amorphization during the cascade. Although large disordered regions result, these retain their basic crystalline structure. These results are in contrast with observations in pure silicon where direct-impact amorphization from the cascade is seen to take place. The SiC results also show anisotropy in the number of Si and C recoils as well as in the number of replacements in each sublattice. Details of the damage configurations obtained will be discussed

  8. Static and dynamic light scattering studies on dilute polyrotaxane solutions

    Kume, Tetsuya; Sakai, Yasuhiro; Mayumi, Koichi; Kidowaki, Masatoshi; Yokoyama, Hideaki; Ito, Kohzo; Araki, Jun

    2009-01-01

    Static and dynamic light scattering measurements were performed for dilute polyrotaxane solutions in different types of solvent systems, i.e. dimethylacetamide (DMAc) or dimethylformamide (DMF) containing 1-6 wt% lithium chloride (LiCl), 1 M aqueous sodium hydroxide (NaOH) and dimethylsulfoxide (DMSO). No aggregation of the polyrotaxane in DMF/LiCl was confirmed in the present study. Radius of gyration of the dissolved polyrotaxane was largest in NaOHaq., followed by values in amide solvents/LiCl and that in DMSO, and was probably dominated not by Coulombic repulsion but by the mutual affinity between solvent and polyrotaxane. Ratio of radius of gyration to hydrodynamic radius suggested the flexible random-coiled conformation in DMSO and relatively more extended, semi-flexible ones in amide solvents/LiCl and NaOHaq. The obtained values of second virial coefficient and weight average molecular weight seemed to be affected by a potential change in differential refractive index increments, caused by selective macrocationization or ionization.

  9. Model Studies of the Dynamics of Bacterial Flagellar Motors

    Bai, Fan; Lo, Chien-Jung; Berry, Richard M.; Xing, Jianhua

    2009-01-01

    Abstract The bacterial flagellar motor is a rotary molecular machine that rotates the helical filaments that propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation, and switching mechanism of the motor. In a previous article, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here, we further analyze that model, showing that 1), the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with latest experiments; 2), with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, as recently observed; and 3), the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwell-time distribution. The predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental procedures for verification. PMID:19383460

  10. Kinetic studies of ICF target dynamics with ePLAS

    Mason, R. J.

    2016-10-01

    The ePLAS code was recently used1 to show that a modeling change from artificial to real viscosity can result in a decrease of the predicted performance of ICF targets. This code typically follows either fluid or PIC electrons with fluid ions in self-consistent E - and B - fields computed by the Implicit Moment Method2. For the present study the ions have instead been run as PIC particles undergoing Krook-like self-collisions. The ePLAS collision model continually redistributes the ion particle properties toward a local Maxwellian, while conserving the mean density, momentum and energy. Whereas the use of real viscosity captures large Knudsen Number effects as the active target dimensions shrink below the ion mean-free-path, the new kinetic modeling can manifest additional effects such as collisional shock precursors3 from the escape and streaming of the fastest particle ions. In 2D cylindrical geometry we will explore how such kinetic shock extensions might affect shell and core compression dynamics in ICF target implosions.

  11. EXPERIMENTAL STUDY OF SHOCK WAVE DYNAMICS IN MAGNETIZED PLASMAS

    Podder, Nirmol K.

    2009-01-01

    In this four-year project (including one-year extension), the project director and his research team built a shock-wave-plasma apparatus to study shock wave dynamics in glow discharge plasmas in nitrogen and argon at medium pressure (1-20 Torr), carried out various plasma and shock diagnostics and measurements that lead to increased understanding of the shock wave acceleration phenomena in plasmas. The measurements clearly show that in the steady-state dc glow discharge plasma, at fixed gas pressure the shock wave velocity increases, its amplitude decreases, and the shock wave disperses non-linearly as a function of the plasma current. In the pulsed discharge plasma, at fixed gas pressure the shock wave dispersion width and velocity increase as a function of the delay between the switch-on of the plasma and shock-launch. In the afterglow plasma, at fixed gas pressure the shock wave dispersion width and velocity decrease as a function of the delay between the plasma switch-off and shock-launch. These changes are found to be opposite and reversing towards the room temperature value which is the initial condition for plasma ignition case. The observed shock wave properties in both igniting and afterglow plasmas correlate well with the inferred temperature changes in the two plasmas

  12. Morphological findings in dynamic swallowing studies of symptomatic patients

    Scharitzer, Martina; Pokieser, Peter; Schober, Ewald; Schima, Wolfgang; Eisenhuber, Edith; Stadler, Alfred; Memarsadeghi, Mazda; Partik, Bernhard; Lechner, Gerhard; Ekberg, Olle

    2002-01-01

    The aim of this study was to assess the role of videofluoroscopy in the detection of structural abnormalities of the pharynx and esophagus in patients with different symptoms of impaired deglutition. Dynamic radiographic recording of deglutition was performed in 3193 consecutive patients (1578 men, 1615 women; mean age 54 years) suffering from dysphagia, suspicion of aspiration, globus sensation, and non-cardiac chest pain. We assessed different structural lesions from the oral cavity to the esophagus and classified them into eight categories. Their frequency and association with the different clinical symptoms were evaluated. Videofluoroscopy revealed 1040 structural abnormalities in 833 patients (26%) including mass lesions from the oral cavity to hyoid/larynx (n=66), pharyngeal diverticula (n=181), pharyngeal masses (n=78), other pharyngeal narrowings (n=71), webs (n=98), masses (n=39), and other narrowings (n=73) of the upper esophageal sphincter, esophageal diverticula (n=80), esophageal webs, rings and strictures (n=194), and intrinsic and extrinsic esophageal lesions (n=160). There was a considerable variance of findings for different symptoms. In a large proportion of symptomatic patients videofluoroscopy detects morphological abnormalities along pharynx and esophagus often combined with functional disorders. This fact underlines the role of videofluoroscopy as a diagnostic test for function as well as morphology. (orig.)

  13. Studying protein assembly with reversible Brownian dynamics of patchy particles

    Klein, Heinrich C. R. [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); Schwarz, Ulrich S., E-mail: ulrich.schwarz@bioquant.uni-heidelberg.de [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); BioQuant, Heidelberg University, 69120 Heidelberg (Germany)

    2014-05-14

    Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly.

  14. MOLECULAR DYNAMICS STUDY OF CYTOCHROME C – LIPID COMPLEXES

    V. Trusova

    2017-10-01

    Full Text Available The interactions between a mitochondrial hemoprotein cytochrome c (cyt c and the model lipid membranes composed of zwitterionic lipid phosphatidylcholine (PC and anionic lipids phosphatidylglycerol (PG, phosphatidylserine (PS or cardiolipin (CL were studied using the method of molecular dynamics. It was found that cyt c structure remains virtually unchanged in the protein complexes with PC/PG or PC/PS bilayers. In turn, protein binding to PC/CL bilayer is followed by the rise in cyt c radius of gyration and root-mean-square fluctuations. The magnitude of these changes was demonstrated to increase with the anionic lipid content. The revealed effect was interpreted in terms of the partial unfolding of polypeptide chain in the region Ala15-Leu32, widening of the heme crevice and enhancement of the conformational fluctuations in the region Pro76-Asp93 upon increasing the CL molar fraction from 5 to 25%. The results obtained seem to be of utmost importance in the context of amyloidogenic propensity of cyt c.

  15. Numerical study of sediment dynamics during hurricane Gustav

    Zang, Zhengchen; Xue, Z. George; Bao, Shaowu; Chen, Qin; Walker, Nan D.; Haag, Alaric S.; Ge, Qian; Yao, Zhigang

    2018-06-01

    In this study, the coupled ocean-atmosphere-wave-and-sediment transport (COAWST) modeling system was employed to explore sediment dynamics in the northern Gulf of Mexico during hurricane Gustav in 2008. The performance of the model was evaluated quantitatively and qualitatively against in-situ and remote sensing measurements, respectively. After Gustav's landfall in coastal Louisiana, the maximum significant wave heights reached more than 8 m offshore and they decreased quickly as it moved toward the inner shelf, where the vertical stratification was largely destroyed. Alongshore currents were dominant westward on the eastern sector of the hurricane track, and offshoreward currents prevailed on the western sector. High suspended sediment concentrations (>1000 mg/l) were confined to the inner shelf at surface layers and the simulated high concentrations at the bottom layer extended to the 200 m isobaths. The stratification was restored one week after landfall, although not fully. The asymmetric hurricane winds induced stronger hydrodynamics in the eastern sector, which led to severe erosion. The calculated suspended sediment flux (SSF) was convergent to the hurricane center and the maximum SSF was simulated near the south and southeast of the Mississippi river delta. The averaged post-hurricane deposition over the Louisiana shelf was 4.0 cm, which was 3.2-26 times higher than the annual accumulation rate under normal weather conditions.

  16. Study of superionic conductors dynamics by continued diffusion model

    Bennai, M.

    1993-12-01

    The superionic conductors form a special category of solids characterized by their remarkable transport properties and are in general, Simplified as being constituted by the superposition of two inter penetrable crystal lattices. The ions of the first one form a rigid structure through which the other ions of opposite charge diffuse in quasi-liquid way. Basing on experimental and theoretical arguments, it was proved necessary to adopt a model of N-body continued diffusion which the basic theory is that of brownian movement. This thesis deals with the study of the dynamic structure factor S (q,w) and its line half width by the method of development in continued fractions issued from the Mori theory. With regard to the analytical difficulty met at the time of the static correlations functions calculation, the homogeneous approximation was applied and the notion of effective strength was introduced. So, it was obtained general relationships which give the static correlation functions, only in term of the static structure factor of liquids and effective potential. 98 refs.; 22 figs. (F.M.)

  17. Comprehensive aerodynamic and dynamic study of independence of ukraine monument

    I. M. Lebedich

    2003-06-01

    Full Text Available Comprehensive approach for solution the engineering problems o f creation the high-rise extended pillartype Monument in Kiyv is described. The results o f dynamic tests o f 1:25 scale model and aerodynamictests o f 1:8 scale model o f the Monument in TAD-2 wind tunnel are given. The procedures fordetermination o f actual dynamic characteristics and assurance the efficiency o f damping on the siteare described

  18. Magnetic Dynamics of Fine Particles Studied by Inelastic Neutron Scattering

    Hansen, Mikkel Fougt; Bødker, Franz; Mørup, Steen

    2000-01-01

    We give an introduction to inelastic neutron scattering and the dynamic scattering function for magnetic nanoparticles. Differences between ferromagnetic and antiferromagnetic nanoparticles are discussed and we give a review of recent results on ferromagnetic Fe nanoparticles and canted antiferro......We give an introduction to inelastic neutron scattering and the dynamic scattering function for magnetic nanoparticles. Differences between ferromagnetic and antiferromagnetic nanoparticles are discussed and we give a review of recent results on ferromagnetic Fe nanoparticles and canted...

  19. Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

    Kaszuba, K.; Postila, P. A.; Cramariuc, O.

    2013-01-01

    studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular...... interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...

  20. Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer

    Casuyac Miqueas

    2016-01-01

    Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.

  1. Modeling the effect of intermolecular force on the size-dependent pull-in behavior of beam-type NEMS using modified couple stress theory

    Beni, Yaghoub Tadi; Karimipour, Iman [Shahrekord University, Shahrekord (Iran, Islamic Republic of); Abadyan, Mohamadreza [Islamic Azad University, Shahrekord (Iran, Islamic Republic of)

    2014-09-15

    Experimental observations reveal that the physical response of nano structures is size-dependent. Herein, modified couple stress theory has been used to study the effect of intermolecular van der Waals force on the size dependent pull-in of nano bridges and nano cantilevers. Three approaches including using differential transformation method, applying numerical method and developing a simple lumped parameter model have been employed to solve the governing equation of the systems. The pull-in parameters i.e. critical tip deflection and instability voltage of the nano structures have been determined. Effect of the van der Waals attraction and the size dependency and the importance of coupling between them on the pull-in performance have been discussed.

  2. Modeling the effect of intermolecular force on the size-dependent pull-in behavior of beam-type NEMS using modified couple stress theory

    Beni, Yaghoub Tadi; Karimipour, Iman; Abadyan, Mohamadreza

    2014-01-01

    Experimental observations reveal that the physical response of nano structures is size-dependent. Herein, modified couple stress theory has been used to study the effect of intermolecular van der Waals force on the size dependent pull-in of nano bridges and nano cantilevers. Three approaches including using differential transformation method, applying numerical method and developing a simple lumped parameter model have been employed to solve the governing equation of the systems. The pull-in parameters i.e. critical tip deflection and instability voltage of the nano structures have been determined. Effect of the van der Waals attraction and the size dependency and the importance of coupling between them on the pull-in performance have been discussed.

  3. Empirical molecular-dynamics study of diffusion in liquid semiconductors

    Yu, W.; Wang, Z. Q.; Stroud, D.

    1996-11-01

    We report the results of an extensive molecular-dynamics study of diffusion in liquid Si and Ge (l-Si and l-Ge) and of impurities in l-Ge, using empirical Stillinger-Weber (SW) potentials with several choices of parameters. We use a numerical algorithm in which the three-body part of the SW potential is decomposed into products of two-body potentials, thereby permitting the study of large systems. One choice of SW parameters agrees very well with the observed l-Ge structure factors. The diffusion coefficients D(T) at melting are found to be approximately 6.4×10-5 cm2/s for l-Si, in good agreement with previous calculations, and about 4.2×10-5 and 4.6×10-5 cm2/s for two models of l-Ge. In all cases, D(T) can be fitted to an activated temperature dependence, with activation energies Ed of about 0.42 eV for l-Si, and 0.32 or 0.26 eV for two models of l-Ge, as calculated from either the Einstein relation or from a Green-Kubo-type integration of the velocity autocorrelation function. D(T) for Si impurities in l-Ge is found to be very similar to the self-diffusion coefficient of l-Ge. We briefly discuss possible reasons why the SW potentials give D(T)'s substantially lower than ab initio predictions.

  4. Groundwater recharge dynamics in unsaturated fractured chalk: a case study

    Cherubini, Claudia; Pastore, Nicola; Giasi, Concetta I.; Allegretti, Nicolaetta M.

    2016-04-01

    The heterogeneity of the unsaturated zone controls its hydraulic response to rainfall and the extent to which pollutants are delayed or attenuated before reaching groundwater. It plays therefore a very important role in the recharge of aquifers and the transfer of pollutants because of the presence of temporary storage zones and preferential flows. A better knowledge of the physical processes in the unsaturated zone would allow an improved assessment of the natural recharge in a heterogeneous aquifer and of its vulnerability to surface-applied pollution. The case study regards the role of the thick unsaturated zone of the Cretaceous chalk aquifer in Picardy (North of France) that controls the hydraulic response to rainfall. In the North Paris Basin, much of the recharge must pass through a regional chalk bed that is composed of a porous matrix with embedded fractures. Different types of conceptual models have been formulated to explain infiltration and recharge processes in the unsaturated fractured rock. The present study analyses the episodic recharge in fractured Chalk aquifer using the kinematic diffusion theory to predict water table fluctuation in response to rainfall. From an analysis of the data, there is the evidence of 1) a seasonal behavior characterized by a constant increase in the water level during the winter/spring period and a recession period, 2) a series of episodic behaviors during the summer/autumn. Kinematic diffusion models are useful for predict preferential fluxes and dynamic conditions. The presented approach conceptualizes the unsaturated flow as a combination of 1) diffusive flow refers to the idealized portion of the pore space of the medium within the flow rate is driven essentially by local gradient of potential; 2) preferential flow by which water moves across macroscopic distances through conduits of macropore length.

  5. Dynamics and diffusive-conformational coupling in polymer bulk samples and surfaces: a molecular dynamics study

    Vree, C; Mayr, S G

    2010-01-01

    The impact of free surfaces on the mobility and conformational fluctuations of model polymer chains is investigated with the help of classical molecular dynamics simulations over a broad temperature range. Below a critical temperature, T*, similar to the critical temperature of the mode coupling theory, the center-of-mass displacements and temporal fluctuations of the radius of gyration of individual chains-as a fingerprint of structural reconfigurations-reveal a strong enhancement close to surfaces, while this effect diminishes with increasing temperature and observation time. Interpreting conformational fluctuations as a random walk in conformational space, identical activation enthalpies for structural reconfigurations and diffusion are obtained within the error bars in the bulk and at the surfaces, thus indicating a coupling of diffusive and conformational dynamics.

  6. Determination of a silane intermolecular force field potential model from an ab initio calculation

    Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng

    2010-01-01

    Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.

  7. Intermolecular G-quadruplex structure-based fluorescent DNA detection system.

    Zhou, Hui; Wu, Zai-Sheng; Shen, Guo-Li; Yu, Ru-Qin

    2013-03-15

    Adopting multi-donors to pair with one acceptor could improve the performance of fluorogenic detection probes. However, common dyes (e.g., fluorescein) in close proximity to each other would self-quench the fluorescence, and the fluorescence is difficult to restore. In this contribution, we constructed a novel "multi-donors-to-one acceptor" fluorescent DNA detection system by means of the intermolecular G-quadruplex (IGQ) structure-based fluorescence signal enhancement combined with the hairpin oligonucleotide. The novel IGQ-hairpin system was characterized using the p53 gene as the model target DNA. The proposed system showed an improved assay performance due to the introduction of IGQ-structure into fluorescent signaling probes, which could inhibit the background fluorescence and increase fluorescence restoration amplitude of fluoresceins upon target DNA hybridization. The proof-of-concept scheme is expected to provide new insight into the potential of G-quadruplex structure and promote the application of fluorescent oligonucleotide probes in fundamental research, diagnosis, and treatment of genetic diseases. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Intermolecular crosslinks mediate aggregation of phospholipid vesicles by pulmonary surfactant-associated protein SAP-35

    Ross, G.R.; Sawyer, J.; Whitsett, J.

    1987-01-01

    Pulmonary surfactant-associated protein, Mr=35,000 (SAP-35) is known to bind phospholipids and is hypothesized to function in the organization of surfactant lipid membranes. SAP-35 has been observed to accelerate the calcium-induced aggregation of phospholipid vesicles. In order to define the molecular domains of SAP-35 which function in phospholipid aggregation, they have measured the light scattering properties (400nm) of purified canine SAP-35-phospholipid vesicle suspensions. Accelerated aggregation of unilamellar vesicles, requires SAP-35 and at least 2mM free calcium. The initial rate of A 400 change is proportional to the amount of native SAP-35 added over lipid:protein molar ratios ranging from 100:1 to 5000:1. Removal of the SAP-35 collagen-like domain and a specific cysteine residue involved in intermolecular disulfide bonding by bacterial collagenase digestion destroys the protein's lipid aggregation activity. Pre-incubation of SAP-35 with dithiothreitol (DTT) under nondenaturing conditions also results in a time-dependent loss of aggregation activity. Sucrose density gradient floatation of SAP-35 with 14 C dipalmitoyl phosphatidycholine labelled vesicles in the absence or presence of DTT suggests retention of SAP-35 lipid binding capacity. These data demonstrate the importance of SAP-35 triple helix and disulfide crosslinking integrity for the aggregation of unilamellar phospholipid vesicles

  9. Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity.

    Scudieri, Paolo; Musante, Ilaria; Gianotti, Ambra; Moran, Oscar; Galietta, Luis J V

    2016-12-08

    TMEM16A and TMEM16B are plasma membrane proteins with Ca 2+ -dependent Cl - channel function. By replacing the carboxy-terminus of TMEM16A with the equivalent region of TMEM16B, we obtained channels with potentiation of channel activity. Progressive shortening of the chimeric region restricted the "activating domain" to a short sequence close to the last transmembrane domain and led to TMEM16A channels with high activity at very low intracellular Ca 2+ concentrations. To elucidate the molecular mechanism underlying this effect, we carried out experiments based on double chimeras, Forster resonance energy transfer, and intermolecular cross-linking. We also modeled TMEM16A structure using the Nectria haematococca TMEM16 protein as template. Our results indicate that the enhanced activity in chimeric channels is due to altered interaction between the carboxy-terminus and the first intracellular loop in the TMEM16A homo-dimer. Mimicking this perturbation with a small molecule could be the basis for a pharmacological stimulation of TMEM16A-dependent Cl - transport.

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

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

    2014-03-01

    The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. MAu2GeS4-Chalcogel (M = Co, Ni): Heterogeneous Intra- and Intermolecular Hydroamination Catalysts

    Davaasuren, Bambar

    2017-08-08

    High surface area macroporous chalcogenide aerogels (chalcogels) MAu2GeS4 (M = Co, Ni) were prepared from K2Au2GeS4 precursor and Co(OAc)2 or NiCl2 by one-pot sol-gel metathesis reactions in aqueous media. The MAu2GeS4-chalcogels were screened for catalytic intramolecular hydroamination of 4-pentyn-1-amine substrate at different temperatures. 87% and 58% conversion was achieved at 100 °C, using CoAu2GeS4- and NiAu2GeS4-chalcogels respectively, and the reaction kinetics follows the first order. It was established that the catalytic performance of the aerogels is associated with the M(2+) centers present in the structure. Intermolecular hydroamination of aniline with 1-R-4-ethynylbenzene (R = -H, -OCH3, -Br, -F) was carried out at 100 °C using CoAu2GeS4-chalcogel catalyst, due to its promising catalytic performance. The CoAu2GeS4-chalcogel regioselectively converted the pair of substrates to respective Markovnikov products, (E)-1-(4-R-phenyl)-N-phenylethan-1-imine, with 38% to 60% conversion.

  12. Argon intermolecular potential from a measurement of the total scattering cross-section

    Wong, Y.W.

    1975-01-01

    An inversion method to obtain accurate intermolecular potentials from experimental total cross section measurements is presented. This method is based on the high energy Massey--Smith approximation. The attractive portion of the potential is represented by a multi-parameter spline function and the repulsive part by a Morse function. The best fit potential is obtained by a least squares minimization based on comparison of experimental cross sections with those obtained by a Fourier transform of the reduced Massey--Smith phase shift curve. An experimental method was developed to obtain the total cross sections needed for the above inversion procedure. In this technique, integral cross sections are measured at various resolutions and the total cross section is obtained by extrapolating to infinite resolution. Experimental results obtained for the Ar--Ar system are in excellent agreement with total cross sections calculated using the Barker-Fisher-Watts potential. Inversion of the data to obtain a potential distinguishable from the BFW-potential requires an extension of the method based on the Massey--Smith approximation to permit use of JWKB phase shifts and was not attempted

  13. MAu2GeS4-Chalcogel (M = Co, Ni): Heterogeneous Intra- and Intermolecular Hydroamination Catalysts

    Davaasuren, Bambar; Emwas, Abdul-Hamid M.; Rothenberger, Alexander

    2017-01-01

    High surface area macroporous chalcogenide aerogels (chalcogels) MAu2GeS4 (M = Co, Ni) were prepared from K2Au2GeS4 precursor and Co(OAc)2 or NiCl2 by one-pot sol-gel metathesis reactions in aqueous media. The MAu2GeS4-chalcogels were screened for catalytic intramolecular hydroamination of 4-pentyn-1-amine substrate at different temperatures. 87% and 58% conversion was achieved at 100 °C, using CoAu2GeS4- and NiAu2GeS4-chalcogels respectively, and the reaction kinetics follows the first order. It was established that the catalytic performance of the aerogels is associated with the M(2+) centers present in the structure. Intermolecular hydroamination of aniline with 1-R-4-ethynylbenzene (R = -H, -OCH3, -Br, -F) was carried out at 100 °C using CoAu2GeS4-chalcogel catalyst, due to its promising catalytic performance. The CoAu2GeS4-chalcogel regioselectively converted the pair of substrates to respective Markovnikov products, (E)-1-(4-R-phenyl)-N-phenylethan-1-imine, with 38% to 60% conversion.

  14. Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit.

    Ceccon, Alberto; Marius Clore, G; Tugarinov, Vitali

    2016-09-01

    In an exchanging system between major and minor species, the transverse paramagnetic relaxation enhancement rate observed on the resonances of the major species (Γ 2 (app) ) is dependent upon the exchange regime between the species. Quantitative analysis of PRE data in such systems typically assumes that the overall exchange rate k ex between the species is fast on the PRE time scale (k ex ≫ Γ2). Recently, we have characterized the kinetics of binding of the model protein ubiquitin to large (LUV) and small (SUV) unilamellar lipid-based nanoparticles or liposomes (Ceccon A, Tugarinov V, Bax A, Clore GM (2016). J Am Chem Soc 138:5789-5792). Building upon these results and taking advantage of a strong paramagnetic agent with an isotropic g-tensor, Gd(3+), we were able to measure intermolecular methyl carbon and proton PREs between paramagnetically-tagged liposomes and ubiquitin. In the limit of fast exchange (k ex ≫ Γ2) the ratio of the apparent proton to carbon methyl PREs, ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ), is equal to the square of the ratio of the gyromagnetic ratios of the two nuclei, (γΗ/γC)(2). However, outside the fast exchange regime, under intermediate exchange conditions (e.g. when Γ2 is comparable in magnitude to k ex) the ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ) ratio provides a reliable measure of the 'true' methyl PREs.

  15. Single-molecule dynamics in nanofabricated traps

    Cohen, Adam

    2009-03-01

    The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

  16. Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics

    Halverson, Jonathan D.; Lee, Won Bo; Grest, Gary S.; Grosberg, Alexander Y.; Kremer, Kurt

    2011-05-01

    Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. The ring melts were found to diffuse faster than their linear counterparts, with both architectures approximately obeying a D ˜ N-2.4 scaling law for large N. The mean-square displacement of the center-of-mass of the rings follows a sub-diffusive behavior for times and distances beyond the ring extension , neither compatible with the Rouse nor the reptation model. The rings relax stress much faster than linear polymers, and the zero-shear viscosity was found to vary as η0 ˜ N1.4 ± 0.2 which is much weaker than the N3.4 behavior of linear chains, not matching any commonly known model for polymer dynamics when compared to the observed mean-square displacements. These findings are discussed in view of the conformational properties of the rings presented in the preceding paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204904 (2011)], 10.1063/1.3587137.

  17. Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies

    Kim, Seonghan; Chang, Rakwoo [Kwangwoon University, Seoul (Korea, Republic of)

    2016-07-15

    Full atomistic molecular dynamics simulations have been performed for model mixture bilayer membrane systems consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) phospholipids to understand the effects of two essential parameters such as lipid composition and temperature on the structural, dynamical, and phase behavior of mixture membrane systems. Although pure DSPC membranes are in the gel-like (L{sub β}' or P{sub β}') phase at 323 K, raising the temperature by only 10 K or replacing 20% of DSPC lipids by DOPC lipids can change the gel-like phase into the completely liquid-crystalline phase (L{sub α}). This phase change is accompanied by dramatic change in both structural properties such as area per lipid, membrane thickness, deuterium order parameter, and tail angle distribution, and dynamics properties such as mobility map. We also observe that the full width at half-maximum (FWHM) data of tail angle distribution as well as area per lipid (or membrane thickness)can be used as order parameters for the membrane phase transition.

  18. Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies

    Kim, Seonghan; Chang, Rakwoo

    2016-01-01

    Full atomistic molecular dynamics simulations have been performed for model mixture bilayer membrane systems consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) phospholipids to understand the effects of two essential parameters such as lipid composition and temperature on the structural, dynamical, and phase behavior of mixture membrane systems. Although pure DSPC membranes are in the gel-like (L_β' or P_β') phase at 323 K, raising the temperature by only 10 K or replacing 20% of DSPC lipids by DOPC lipids can change the gel-like phase into the completely liquid-crystalline phase (L_α). This phase change is accompanied by dramatic change in both structural properties such as area per lipid, membrane thickness, deuterium order parameter, and tail angle distribution, and dynamics properties such as mobility map. We also observe that the full width at half-maximum (FWHM) data of tail angle distribution as well as area per lipid (or membrane thickness)can be used as order parameters for the membrane phase transition.

  19. A Comparative Study of Three Methodologies for Modeling Dynamic Stall

    Sankar, L.; Rhee, M.; Tung, C.; ZibiBailly, J.; LeBalleur, J. C.; Blaise, D.; Rouzaud, O.

    2002-01-01

    During the past two decades, there has been an increased reliance on the use of computational fluid dynamics methods for modeling rotors in high speed forward flight. Computational methods are being developed for modeling the shock induced loads on the advancing side, first-principles based modeling of the trailing wake evolution, and for retreating blade stall. The retreating blade dynamic stall problem has received particular attention, because the large variations in lift and pitching moments encountered in dynamic stall can lead to blade vibrations and pitch link fatigue. Restricting to aerodynamics, the numerical prediction of dynamic stall is still a complex and challenging CFD problem, that, even in two dimensions at low speed, gathers the major difficulties of aerodynamics, such as the grid resolution requirements for the viscous phenomena at leading-edge bubbles or in mixing-layers, the bias of the numerical viscosity, and the major difficulties of the physical modeling, such as the turbulence models, the transition models, whose both determinant influences, already present in static maximal-lift or stall computations, are emphasized by the dynamic aspect of the phenomena.

  20. Study of spatially extended dynamical systems using probabilistic cellular automata

    Vanag, Vladimir K

    1999-01-01

    Spatially extended dynamical systems are ubiquitous and include such things as insect and animal populations; complex chemical, technological, and geochemical processes; humanity itself, and much more. It is clearly desirable to have a certain universal tool with which the highly complex behaviour of nonlinear dynamical systems can be analyzed and modelled. For this purpose, cellular automata seem to be good candidates. In the present review, emphasis is placed on the possibilities that various types of probabilistic cellular automata (PCA), such as DSMC (direct simulation Monte Carlo) and LGCA (lattice-gas cellular automata), offer. The methods are primarily designed for modelling spatially extended dynamical systems with inner fluctuations accounted for. For the Willamowskii-Roessler and Oregonator models, PCA applications to the following problems are illustrated: the effect of fluctuations on the dynamics of nonlinear systems; Turing structure formation; the effect of hydrodynamic modes on the behaviour of nonlinear chemical systems (stirring effects); bifurcation changes in the dynamical regimes of complex systems with restricted geometry or low spatial dimension; and the description of chemical systems in microemulsions. (reviews of topical problems)