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1

Energy decomposition analysis of covalent bonds and intermolecular interactions.  

Science.gov (United States)

An energy decomposition analysis method is implemented for the analysis of both covalent bonds and intermolecular interactions on the basis of single-determinant Hartree-Fock (HF) (restricted closed shell HF, restricted open shell HF, and unrestricted open shell HF) wavefunctions and their density functional theory analogs. For HF methods, the total interaction energy from a supermolecule calculation is decomposed into electrostatic, exchange, repulsion, and polarization terms. Dispersion energy is obtained from second-order Møller-Plesset perturbation theory and coupled-cluster methods such as CCSD and CCSD(T). Similar to the HF methods, Kohn-Sham density functional interaction energy is decomposed into electrostatic, exchange, repulsion, polarization, and dispersion terms. Tests on various systems show that this algorithm is simple and robust. Insights are provided by the energy decomposition analysis into H(2), methane C-H, and ethane C-C covalent bond formation, CH(3)CH(3) internal rotation barrier, water, ammonia, ammonium, and hydrogen fluoride hydrogen bonding, van der Waals interaction, DNA base pair formation, BH(3)NH(3) and BH(3)CO coordinate bond formation, Cu-ligand interactions, as well as LiF, LiCl, NaF, and NaCl ionic interactions. PMID:19586091

Su, Peifeng; Li, Hui

2009-07-01

2

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2012-04-28

3

Vacuum fluctuations and intermolecular interactions  

International Nuclear Information System (INIS)

The electromagnetic field operators in the vicinity of a neutral molecule are obtained in the Heisenberg picture. The fields are found using the multipolar Hamiltonian and the interaction includes electric dipole, magnetic dipole, electric quadrupole, and diamagnetic couplings. These fields are used to calculate the dispersion energy between two neutral molecules. The dispersion energy may be obtained by treating one molecule as a test body and calculating its response to the field of the other. A note-worthy feature of this test-body approach is that the energy expressions so obtained are valid for all intermolecular separations outside overlap and retardation effects are fully taken into account. The method is applied to the calculation of dispersion energy between a pair of molecules with different polarizability characteristics. The contribution of the diamagnetic coupling to the energy shift is also presented. The theory is adapted to the calculation of N-molecule dispersion interactions and applied to 3- and 4-molecule systems. (orig.)

4

Interaction energies in non-covalently bound intermolecular complexes derived using the subsystem formulation of density functional theory  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Interaction energies for a representative sample of 39 intermolecular complexes are calculated using two computational approaches based on the subsystem formulation of density functional theory introduced by Cortona (Phys. Rev. B 44:8454, 1991), adopted for studies of intermolecular complexes (Wesolowski and Weber in Chem. Phys. Lett. 248:71, 1996). The energy components (exchange-correlation and non-additive kinetic) expressed as explicit density functionals are approximated by means of grad...

Dulak, Marcin; Wesolowski, Tomasz Adam

2007-01-01

5

Local intermolecular interactions for selective CO2 capture by zeolitic imidazole frameworks: energy decomposition analysis  

International Nuclear Information System (INIS)

Intermolecular energy decomposition analysis (EDA) is reported for the binding of CO2 with zeolitic imidazole frameworks (ZIF) to provide a molecular level interpretation of the recent capacity and selectivity measurements of several ZIFs and to suggest a theoretical guideline to improve their performance further, using 1 nm size of organic linker fragment of the ZIFs as a target molecule. The EDA suggests that the local electronic interaction of CO2 and the substituent groups, mainly frozen density and polarization interactions with little charge transfer, is the primary binding interaction, but the electron correlation effects can be equally or more important depending on the binding geometry and functional groups. The present correlated calculations identify the preferred ZIF binding sites for various gases including CO2 to be mostly near the benzene substituent groups rather than the plane of imidazole rings. We predict that the NH2-substituted ZIF would have an enhanced capacity of CO2 as compared to the NO2-substituted ZIF that was recently synthesized and reported to be one of the materials with the best capacity results along with high gas selectivity. The present calculations may imply that the local functionality of the linking organics, rather than detailed framework structures, may be of primary importance in designing certain high capacity MOF or ZIF materials.F materials.

6

Interaction energies in non-covalently bound intermolecular complexes derived using the subsystem formulation of density functional theory.  

Science.gov (United States)

Interaction energies for a representative sample of 39 intermolecular complexes are calculated using two computational approaches based on the subsystem formulation of density functional theory introduced by Cortona (Phys. Rev. B 44:8454, 1991), adopted for studies of intermolecular complexes (Wesolowski and Weber in Chem. Phys. Lett. 248:71, 1996). The energy components (exchange-correlation and non-additive kinetic) expressed as explicit density functionals are approximated by means of gradient-free- (local density approximation) of gradient-dependent- (generalized gradient approximation) approximations. The sample of the considered intermolecular complexes was used previously by Zhao and Truhlar to compare the interaction energies derived using various methods based on the Kohn-Sham equations with high-level quantum chemistry results considered as the reference. It stretches from rare gas dimers up to strong hydrogen bonds. Our results indicate that the subsystem-based methods provide an interesting alternative to that based on the Kohn-Sham equations. Local density approximation, which is the simplest approximation for the relevant density functionals and which does not rely on any empirical data, leads to a computational approach comparing favorably with more than twenty methods based on the Kohn-Sham equations including the ones, which use extensively empirical parameterizations. For various types of non-bonding interactions, the strengths and weaknesses of gradient-free and gradient-dependent approximations to exchange-correlation and non-additive kinetic energy density functionals are discussed in detail. PMID:17354013

Du?ak, Marcin; Weso?owski, Tomasz A

2007-07-01

7

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

Science.gov (United States)

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

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

2014-08-01

8

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2014-08-14

9

Intermolecular Interaction Energies in Molecular Crystals: Comparison and Agreement of Localized Moller-Plesset 2, Dispersion-Corrected Density Functional, and Classical Empirical Two-Body Calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A comparative analysis of the intermolecular energy for a data set including 60 molecular crystals with a large variety of functional groups has been carried out using three different computational approaches: (i) a method based on a physically meaningful empirical partition of the interaction energy (PIXEL), (ii) density functional methods with a posteriori empirical correction for the dispersion interactions (DFT-D), and (iii) a full periodic ab initio quantum mechanical method based on Mol...

Ugliengo, Piero; Civalleri, Bartolomeo; Maschio, Lorenzo

2011-01-01

10

Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET)  

DEFF Research Database (Denmark)

The calcium-sensing receptor (CaR) belongs to family C of the G-protein coupled receptor superfamily. The receptor is believed to exist as a homodimer due to covalent and non-covalent interactions between the two amino terminal domains (ATDs). It is well established that agonist binding to family C receptors takes place at the ATD and that this causes the ATD dimer to twist. However, very little is known about the translation of the ATD dimer twist into G-protein coupling to the 7 transmembrane moieties (7TMs) of these receptor dimers. In this study we have attempted to delineate the agonist-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. Stable and highly receptor-specific BRET signals were obtained in tsA cells transfected with Rluc- and GFP2-tagged CaRs under basal conditions, indicating that CaR is constitutively dimerized. However, the signals were not enhanced by the presence of agonist. These results could indicate that at least parts of the two 7TMs of the CaR homodimer are in close proximity in the inactivated state of the receptor and do not move much relative to one another upon agonist activation. However, we cannot exclude the possibility that the BRET technology is unable to register putative conformational changes in the CaR homodimer induced by agonist binding because of the bulk sizes of the Rluc and GFP2 molecules.

Jensen, Anders A.; Hansen, Jakob L

2002-01-01

11

The diversity of physical forces and mechanisms in intermolecular interactions.  

Science.gov (United States)

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

Berezovsky, Igor N

2011-06-01

12

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

International Nuclear Information System (INIS)

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

13

How molecules stick together in organic crystals: weak intermolecular interactions.  

Science.gov (United States)

This tutorial review introduces the fundamentals of intermolecular interactions in terms of the underlying physics and goes on to illustrate the most popular methods for the computer simulation of intermolecular interactions, from atom-atom potentials to ab initio methods, including intermediate, hybrid methods, with an appreciation of their relative merits and costs. Typical results are critically presented, culminating in the most difficult exercise of all, the computer prediction of crystal structures. Perspectives on our present and future ability to understand and exploit intermolecular interactions are given. PMID:19690742

Dunitz, Jack D; Gavezzotti, Angelo

2009-09-01

14

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

Science.gov (United States)

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

Xantheas, Sotiris S.; Werhahn, Jasper C.

2014-08-01

15

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

Energy Technology Data Exchange (ETDEWEB)

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

Xantheas, Sotiris S.; Werhahn, Jasper C.

2014-08-14

16

Intermolecular interactions and the thermodynamic properties of supercritical fluids  

Science.gov (United States)

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

Yigzawe, Tesfaye M.; Sadus, Richard J.

2013-05-01

17

Spectral manifestation of intermolecular interaction in phthalimide and isatin dimers  

Science.gov (United States)

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

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

2010-03-01

18

Spectral manifestation of intermolecular interaction in phthalimide and isatin dimers  

International Nuclear Information System (INIS)

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

19

Intermolecular interaction energies in molecular crystals: comparison and agreement of localized Møller-Plesset 2, dispersion-corrected density functional, and classical empirical two-body calculations.  

Science.gov (United States)

A comparative analysis of the intermolecular energy for a data set including 60 molecular crystals with a large variety of functional groups has been carried out using three different computational approaches: (i) a method based on a physically meaningful empirical partition of the interaction energy (PIXEL), (ii) density functional methods with a posteriori empirical correction for the dispersion interactions (DFT-D), and (iii) a full periodic ab initio quantum mechanical method based on Møller-Plesset perturbation theory for the electron correlation using localized crystal orbitals (LMP2). Due to the large computational cost, LMP2 calculations have been restricted to a subset of seven molecular crystal comprising benzene, formic acid, formamide, succinic anhydride, urea, oxalic acid, and nitroguanidine, and the results compared with PIXEL and DFT-D data as well as with the experimental data show excellent agreement among all adopted methods. This shows that both DFT-D and PIXEL approaches are robust predictive tools for studying molecular crystals. A detailed analysis shows a very similar dispersion contribution of the two methods across the 60 considered molecular crystals. The study also confirms that pure DFT shows serious deficiencies in properly handling molecular crystals in which the dispersive contribution is large. Due to the negligible requested computational resources, PIXEL is the method of choice in screening of a large number of molecular crystals, an essential step to predict crystal polymorphism or to study crystal growth processes. DFT-D can then be used to refine the ranking emerged from PIXEL calculations due to its general applicability and robustness in properly handling short-range interactions. PMID:21894880

Maschio, Lorenzo; Civalleri, Bartolomeo; Ugliengo, Piero; Gavezzotti, Angelo

2011-10-20

20

Intermolecular forces: A solution to dispersion interactions  

Science.gov (United States)

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

Shimizu, Ken D.

2013-12-01

 
 
 
 
21

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

Science.gov (United States)

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

Korona, Tatiana

2008-11-21

22

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

Science.gov (United States)

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

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

2008-10-01

23

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

DEFF Research Database (Denmark)

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

Munteanu, Cristian R.; Henriksen, Christian

2013-01-01

24

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

Science.gov (United States)

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

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

2014-10-23

25

Weak intermolecular interactions in gas-phase NMR  

CERN Document Server

Gas-phase NMR spectra demonstrating the effect of weak intermolecular forces on the NMR shielding constants of the interacting species are reported. We analyse the interaction of the molecular hydrogen isotopomers with He, Ne, and Ar, and the interaction in the He-CO_2 dimer. The same effects are studied for all these systems in the ab initio calculations. The comparison of the experimental and computed shielding constants is shown to depend strongly on the treatment of the bulk susceptibility effects, which determine in practice the pressure dependence of the experimental values. Best agreement of the results is obtained when the bulk susceptibility correction in rare gas solvents is evaluated from the analysis of the He-rare gas interactions, and when the shielding of deuterium in D_2-rare gas systems is considered.

Garbacz, Piotr; Jackowski, Karol; Moszynski, Robert; Jaszunski, Michal

2011-01-01

26

Effects of intermolecular interaction on inelastic electron tunneling spectra  

Science.gov (United States)

We have examined the effects of intermolecular interactions on the inelastic electron tunneling spectroscopy (IETS) of model systems: a pair of benzenethiol or a pair of benzenedithiol sandwiched between gold electrodes. The dependence of the IETS on the mutual position of and distance between the paired molecules has been predicted and discussed in detailed. It is shown that, although in most cases, there are clear spectral fingerprints present which allow identification of the actual structures of the molecules inside the junction. Caution must be exercised since some characteristic lines can disappear at certain symmetries. The importance of theoretical simulation is emphasized.

Kula, Mathias; Luo, Yi

2008-02-01

27

Raman study on intermolecular and ionic interactions in gel electrolytes  

Science.gov (United States)

Raman spectroscopy was applied to investigate the intermolecular interactions in multi-component gel electrolytes consisting of ethylene carbonate and propylene carbonate, (EC-PC) mixed solvent, lithium salt and PMMA polymeric matrix. It is shown that triflate anions tend to essential aggregation in the EC/PC solvent, which results in a worsening of both mechanical and conductive properties of the gel. It is also found that PMMA-based gels with low salt concentration show an obvious macroscopic phase separation, and the spectroscopic characterization of the different phases is presented.

Adebahr, J.; Gavelin, P.; Ostrovskii, D.; Torell, L. M.; Wesslen, B.

1999-05-01

28

Control of emission by intermolecular fluorescence resonance energy transfer and intermolecular charge transfer.  

Science.gov (United States)

Control of emission by intermolecular fluorescence resonant energy transfer (IFRET) and intermolecular charge transfer (ICT) is investigated with the quantum-chemistry method using two-dimensional (2D) and three-dimensional (3D) real space analysis methods. The work is based on the experiment of tunable emission from doped 1,3,5-triphenyl-2-pyrazoline (TPP) organic nanoparticles (Peng, A. D.; et al. Adv. Mater. 2005, 17, 2070). First, the excited-state properties of the molecules, which are studied (TPP and DCM) in that experiment, are investigated theoretically. The results of the 2D site representation reveal the electron-hole coherence and delocalization size on the excitation. The results of 3D cube representation analysis reveal the orientation and strength of the transition dipole moments and intramolecular or intermolecular charge transfer. Second, the photochemical quenching mechanism via IFRET is studied (here "resonance" means that the absorption spectrum of TPP overlaps with the fluorescence emission spectrum of DCM in the doping system) by comparing the orbital energies of the HOMO (highest occupied molecular orbital) and the LUMO (lowest unoccupied molecular orbital) of DCM and TPP in absorption and fluorescence. Third, for the DCM-TPP complex, the nonphotochemical quenching mechanism via ICT is investigated. The theoretical results show that the energetically lowest ICT state corresponds to a pure HOMO-LUMO transition, where the densities of the HOMO and LUMO are strictly located on the DCM and TPP moieties, respectively. Thus, the lowest ICT state corresponds to an excitation of an electron from the HOMO of DCM to the LUMO of TPP. PMID:16686468

Sun, Mengtao; Pullerits, Tõnu; Kjellberg, Pär; Beenken, Wichard J D; Han, Keli

2006-05-18

29

Evolutionary meandering of intermolecular interactions along the drift barrier.  

Science.gov (United States)

Many cellular functions depend on highly specific intermolecular interactions, for example transcription factors and their DNA binding sites, microRNAs and their RNA binding sites, the interfaces between heterodimeric protein molecules, the stems in RNA molecules, and kinases and their response regulators in signal-transduction systems. Despite the need for complementarity between interacting partners, such pairwise systems seem to be capable of high levels of evolutionary divergence, even when subject to strong selection. Such behavior is a consequence of the diminishing advantages of increasing binding affinity between partners, the multiplicity of evolutionary pathways between selectively equivalent alternatives, and the stochastic nature of evolutionary processes. Because mutation pressure toward reduced affinity conflicts with selective pressure for greater interaction, situations can arise in which the expected distribution of the degree of matching between interacting partners is bimodal, even in the face of constant selection. Although biomolecules with larger numbers of interacting partners are subject to increased levels of evolutionary conservation, their more numerous partners need not converge on a single sequence motif or be increasingly constrained in more complex systems. These results suggest that most phylogenetic differences in the sequences of binding interfaces are not the result of adaptive fine tuning but a simple consequence of random genetic drift. PMID:25535374

Lynch, Michael; Hagner, Kyle

2015-01-01

30

Competitive intra- and intermolecular interactions in secondary Mannich bases  

Science.gov (United States)

The secondary Mannich base 2-(N-cyclohexylaminomethyl)-4-methyl-phenol ( 1) was synthesized. The crystal structure was determined whereby linear chains through N sbnd H⋯O hydrogen bonds were detected between molecules containing typical chelate rings with intramolecular O sbnd H⋯N hydrogen bonds, as in the traditionally studied tertiary Mannich bases. The N⋯O distance appeared much shorter, i.e. 2.614 and 2.601 Å in the two conformers in the chain, in comparison to tertiary Mannich bases [1]. Extensive experimental and theoretical studies on aggregation in solution and in the gas phase (by DFT B3LYP/6-31+G(d,p) calculations) were undertaken. It was shown self-aggregation is weak even in weakly polar CCl 4 solvent. Up to the concentration 0.3 mol/dm 3, as follows from dipole moment and average molecular weight investigations, there are only monomers of structure resembling those detected in the solid state. The experiments at higher concentrations as well as theoretical calculations proved the postulate that the specific strong intramolecular hydrogen bond found in the solid state of secondary Mannich bases results from intermolecular interactions.

Ko?odziejczak, Jerzy; Adamczyk-Wo?niak, Agnieszka; Sporzy?ski, Andrzej; Kochel, Andrzej; Koll, Aleksander

2010-07-01

31

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

Science.gov (United States)

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

McKenzie, S; Kang, H C

2014-12-21

32

Evaluation of intermolecular interaction potential using regularization method. 3. Interaction of argon, krypton and xenon atoms  

International Nuclear Information System (INIS)

Evaluations of interaction potential of argon, krypton and xenon atoms were obtained on the basis of experimental data on the second virial coefficient using regularization method. It is shown that the method enables to obtain from temperature dependence of the second virial coefficient a rather exhaustive information about the potential of intermolecular interaction and to reproduce exactly the part of potential function, which corresponds to potential pit and is the most sensitive to the second virial coefficient. 16 refs., 2 figs., 3 tabs

33

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

Science.gov (United States)

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

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

2012-07-01

34

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

Science.gov (United States)

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

Kajiya, Daisuke; Saitow, Ken-ichi

2010-07-01

35

Intermolecular interactions in poly(vinylidene fluoride) and ?-caprolactam mixtures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Mixtures of poly(vinylidene fluoride) (PVDF) and caprolactam (CPL) have been investigated as models for possible cross-interactions between vinylidene fluoride and amide structural units, that might account for the very fine phase morphology previously observed in PVDF/polyamide 6 blends. Over the entire composition range, the PVDF/CPL mixtures are monophase above the PVDF melting temperature. From the depression of the PVDF melting point, a negative interaction energy density, B, has been ca...

Liu, Zehui; Mare?chal, Philippe; Je?ro?me, Robert

1996-01-01

36

Double strand interaction is the predominant pathway for intermolecular recombination of adeno-associated viral genomes  

International Nuclear Information System (INIS)

Intermolecular recombination is the foundation for dual vector mediated larger gene transfer by recombinant adeno-associated virus (rAAV). To identify precursors for intermolecular recombination, we sequentially infected skeletal muscle with AAV LacZ trans-splicing viruses. At 1 month postinfection, nearly all inputting single-strand (ss) AAV genomes were cleared out in muscle. If ss-ss interaction is absolutely required for intermolecular recombination, LacZ expression from sequential infection will be negligible to that from coinfection. Interestingly, expression from sequential infection reached ?50% of that from coinfection at the 1-month time-point in BL6 mice. In immune deficient SCID mice, expression from sequential infection was comparable to that from coinfection at the 4- and 13-month time points. Our results suggest that ds interaction represents the predominant pathway for AAV intermolecular recombination

37

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

Science.gov (United States)

The nature and strength of the intermolecular interactions in the solutions of three azo-benzene derivatives (ADi, i=1, 2, 3) were established by solvatochromic effects in solvents with different electric permittivities, refractive indices and Kamlet-Taft constants. A quantum mechanical analysis corroborated with spectral data offered information about the excited state dipole moments and polarizabilities of the studied compounds. The separation of the supply of universal and specific interactions to the total spectral shift was made based on the regression coefficients from the equations describing the solvatochromic effect. Supplementary information about the composition of the first solvation shell and the energy in the solute-solvent molecular pairs were obtained analyzing the ternary solutions of ADi, i=1, 2, 3 compounds in solvent mixture Methanol (M)+n-Hexane (H). PMID:25168003

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

2015-02-01

38

Reversible electron-induced cis-trans isomerization mediated by intermolecular interactions  

International Nuclear Information System (INIS)

Reversible isomerization processes are rarely found when organic molecular switches are adsorbed on metal surfaces. One obstacle is the large energy difference of the isomeric forms, since usually the most planar conformer has the largest adsorption energy. In the example of an imine derivative, we show a strategy for also stabilizing the non-planar isomer by intermolecular bonding to its neighbors. Tunneling electrons from the tip of a scanning tunneling microscope can then be used to induce reversible switching between the trans and cis-like state. Supported by model force-field calculations, we illustrate that the most probable cause of the enhanced stability of the three-dimensional cis state at specific adsorption sites is the electrostatic interaction with N sites of the neighboring molecule.

39

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

CERN Document Server

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

Zhu, Wuming; Savin, Andreas; Angyán, János G

2014-01-01

40

Intermolecular interactions in mixtures of ethyl formate with methanol, ethanol, and 1-propanol on density, viscosity, and ultrasonic data  

Science.gov (United States)

Density (?), viscosity (?), and ultrasonic velocity ( U) have been measured for binary mixtures of ethyl formate with methanol, ethanol, and 1-propanol at 303 K. From the experimental data, adiabatic compressibility (?), acoustic impedance ( Z), viscous relaxation time (?), free length ( L f), free volume ( V f), internal pressure (?i), and Gibbs free energy (? G) have been deduced. It is shown that strength of intermolecular interactions between ethyl formate with selected 1-alcohols were in the order of methanol < ethanol < 1-propanol.

Elangovan, S.; Mullainathan, S.

2014-12-01

 
 
 
 
41

Theoretical study on intermolecular interactions between furan and dihalogen molecules XY(X,Y=F,Cl,Br)  

Science.gov (United States)

Equilibrium geometries, interaction energies, atomic charge, and charge transfer for the intermolecular interactions between furan and dihalogen molecules XY(X; Y =F,Cl,Br) were studied at the MP2/aug-cc-pVDZ level. Three types of geometry are observed in these interactions: the ?-type geometry (I), in which the XY lies above the furan ring and almost perpendicularly to the C4-C5 bond of furan; the ?-type geometry (II), where the X atom is pointed toward the nonbonding electron pair (n pair) of oxygen atom in furan; and the ?-type geometry (III), describing a blueshift hydrogen bond formed between the hydrogen atom of furan and dihalogen molecules XY. The calculated interaction energies show that the ?-type structures are more stable than the corresponding ?-type and ?-type structures. To study the nature of the intermolecular interactions, an energy decomposition analysis was carried out and the results indicate that both the ?-type and ?-type interactions are dominantly inductive energy in nature, while dispersion energy governs the ?-type interactions.

Wang, Zhao-Xu; Zhang, Jing-Chang; Wu, Jun-Yong; Cao, Wei-Liang

2007-04-01

42

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

Science.gov (United States)

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

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

2014-08-01

43

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

Science.gov (United States)

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

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

2014-08-14

44

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

DEFF Research Database (Denmark)

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 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 Institute of Physics. [http://dx.doi.org/10.1063/1.4742153

Cybulski, Hubert; Fernandez, Berta

2012-01-01

45

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

Science.gov (United States)

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

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

2014-02-21

46

Intermolecular interactions and tautomerism of nucleic acid bases and their analogues  

Science.gov (United States)

The structures and stabilization energies of guanine—cytosine, guanine—thymine and adenine—thymine base pairs formed by "normal" amino-oxo and "rare" amino-hydroxy tautomers of guanine and the "normal" tautomers of adenine and thymine are studied using a combined quantum-mechanical approach, an ab initio calculation for relative stabilities of the isolated tautomers together with a calculation of intermolecular interaction energies using a multipolar expansion method developed by Claverie and co-workers. It is shown that the interaction between the components of the base pairs decreases the relative stability of the pairs involving "rare" tautomers of guanine; for the isolated molecules the stability of both tautomers of guanine is found to be approximately the same. Our calculations include the base pairs formed by the "rare" hydroxy tautomer of guanine, whose existence has been reported in recent experimental studies of guanines isolated in an inert low-temperature matrix. Calculations for this amino-hydroxy form of guanine serve as a model for interactions of O6-methylguanine with pyrimidine bases.

Czerminski, R.; Szczepaniak, K.; Person, W. B.; Kwiatkowski, J. S.

1990-09-01

47

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

Science.gov (United States)

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

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

2009-09-01

48

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

The mutated hemoglobin HbC (beta 6 Glu-->Lys), in the oxygenated (R) liganded state, forms crystals inside red blood cells of patients with CC and SC diseases. Static and dynamic light scattering characterization of the interactions between the R-state (CO) HbC, HbA, and HbS molecules in low-ionic-strength solutions showed that electrostatics is unimportant and that the interactions are dominated by the specific binding of solutions' ions to the proteins. Microscopic observations and determin...

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

2002-01-01

49

The Study of Intermolecular Interactions Using Optical Biosensors Operating on the Effect of Surface Plasmon Resonance  

Directory of Open Access Journals (Sweden)

Full Text Available Present knowledge of the technology of optical biosensors based on the effect of surface plasmon resonance (SPR is presented. SPR enables to register almost all molecular interactions in real time without any labels or associated processes. There are considered the main technical characteristics of SPR biosensors and the principles of analysis of kinetic, equilibrium and thermodynamic parameters of intermolecular interactions.There are presented a number of examples of Biacore biosensors (GE Healthcare, USA application in post-genomic researches carried out in the Institute of Biomedical Chemistry (Moscow, Russia: SPR technology has been used in the analysis of intermolecular interactions, like protein-protein, protein-low-molecular-weight compounds, protein-DNA; in the analysis of protein oligomerization and the search of dimerization inhibitors; in the search of drug prototype compounds interacting with a target protein; and in biosensor analysis of disease biomarkers.The technology of optical biosensors operating on the effect of surface ?lasmon resonance is getting one of the approaches in researching various intermolecular interactions. It is of universal character and enables to record the interactions between almost any molecular objects in a wide range of concentrations. SPR-biosensors have very high accuracy, capability of reproducing and sensitivity; due to these characteristics their application is growing both in fundamental and applied researches.

?.S. Ivanov

2012-12-01

50

Atom depth analysis delineates mechanisms of protein intermolecular interactions  

International Nuclear Information System (INIS)

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

51

Atom depth analysis delineates mechanisms of protein intermolecular interactions  

Energy Technology Data Exchange (ETDEWEB)

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

Alocci, Davide, E-mail: alodavide@gmail.com [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Bernini, Andrea, E-mail: andrea.bernini@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Niccolai, Neri, E-mail: neri.niccolai@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); SienaBioGrafix Srl, via A. Fiorentina 1, 53100 Siena (Italy)

2013-07-12

52

Redetermined structure, intermolecular interactions and absolute configuration of royleanone  

Directory of Open Access Journals (Sweden)

Full Text Available The structure of the title diterpenoid, C20H28O3, {systematic name: (4bS,8aS-3-hydroxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthrene-1,4-dione} is confirmed [Eugster et al. (1993. Private communication (refcode HACGUN. CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclohexane ring adopts a chair conformation whereas the other cyclohexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intramolecular O—H...O hydrogen bond generates an S(5 ring motif. In the crystal, molecules are linked into chains along [010] by O—H...O hydrogen bonds and weak C—H...O interactions. The packing also features C...O [3.131?(3?Å] short contacts.

Hoong-Kun Fun

2011-05-01

53

Intermolecular Interaction in the Binary Mixture of valine with Water at 303.15 K  

Directory of Open Access Journals (Sweden)

Full Text Available The ultrasonic velocity (u, density (? and viscosity (? have been measured at 2 MHz frequency in the binary mixtures of valine with water over entire range concentration at 303.15 K using ultrasonic interferometer technique. The experimental data have been used to calculate acoustical parameter namely adiabatic compressibility (?a, acoustic impedance (z, intermolecular free length (Lf and relative association (RA with a view to investigate the nature and strength of molecular interaction in the binary liquid mixture. The obtained result support the occurrence of complex formation through intermolecular hydrogen bonding in there binary liquid mixtures and further used to interpret the hydrophilic part of the solute and molecular interactions in the solutions.

S.Mirikar

2014-12-01

54

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

General microscopic mechanism of ferroelectric ordering in chiral smectic C* liquid crystals is considered. It is shown that if the mesogenic molecules have a sufficiently low symmetry, the spontaneous polarization is proportional to one of the biaxial vector order parameters of the smectic C phase. This order parameter may be determined by intermolecular interactions which are not sensitive to molecular chirality. At the same time, the polarization is also proportional to a...

Osipov, M. A.; Gorkunov, M. V.

2007-01-01

55

Intermolecular Interactions in Dye-Sensitized Solar Cells: A Computational Modeling Perspective  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present a unified overview of our recent activity on the modeling of relevant intermolecular interactions occurring in dye-sensitized solar cells (DSCs). The DSC is an inherent complex system, whose efficiency is essentially determined by the interrelated phenomena occurring at the multiple molecular?semiconductor?electrolyte heterointerfaces. In this Perspective, we illustrate the basic methodology and selected applications of computational modeling of dye?dye and dye...

Pastore, Mariachiara; Angelis, Filippo

2013-01-01

56

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

International Nuclear Information System (INIS)

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

57

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2013-08-15

58

Intermolecular potential energy surface and thermophysical properties of ethylene oxide  

Science.gov (United States)

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

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

2014-10-01

59

Intermolecular potential energy surface and thermophysical properties of ethylene oxide  

International Nuclear Information System (INIS)

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

60

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

Science.gov (United States)

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

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

2014-08-14

 
 
 
 
61

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2011-06-30

62

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

Science.gov (United States)

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

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

2014-12-01

63

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

Science.gov (United States)

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

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

2013-08-01

64

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

Science.gov (United States)

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

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

2014-10-01

65

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

Science.gov (United States)

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

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

2014-10-01

66

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

Science.gov (United States)

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

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

2013-11-01

67

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

Science.gov (United States)

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

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

2014-12-23

68

Structural study of citrate layers on gold nanoparticles: role of intermolecular interactions in stabilizing nanoparticles.  

Science.gov (United States)

The structure of citrate adlayers on gold nanoparticles (AuNPs) was investigated. Infrared (IR) and X-ray photoelectron spectroscopy (XPS) analyses indicate citrate anions are adsorbed on AuNPs through central carboxylate groups. A unique structure of adsorbed citrate is determined, and a pH-induced structural transition is presented. IR analysis probes dangling dihydrogen anions (H2Citrate(-)) and hydrogen bonding of carboxylic acid groups between adsorbed and dangling citrate anions. A contribution of steric repulsion between citrate layers to particle stability is characterized. Structure-based modeling, which is consistent with scanning tunneling microscopy (STM) and transmission electron microscopy (TEM) images in the literature, suggests organization details relating to the formation of self-assembled layers on (111), (110), and (100) surfaces of AuNPs. Adsorption characteristics of the citrate layer include the interaction between hydrogen-bonded citrate chains, bilayer formation, surface coverage, and chirality. The enthalpic gain from intermolecular interactions and the importance of molecular structure/symmetry on the adsorption are discussed. Combining the enthalpic factor with surface diffusion and adsorption geometry of (1,2)-dicarboxyl fragments on Au(111), H2Citrate(-) anions effectively stabilize the (111) surface of the AuNPs. The detailed understanding of intermolecular interactions in the molecular adlayer provides insight for nanoparticle formation and stabilization. We expect these findings will be relevant for other nanoparticles stabilized by hydroxy carboxylate-based amino acids and have broad implications in NP-based interfacial studies and applications. PMID:24422457

Park, Jong-Won; Shumaker-Parry, Jennifer S

2014-02-01

69

The Molecular Oxygen Tetramer: Intermolecular Interactions and Implications for the $\\epsilon$ Solid Phase  

CERN Document Server

Recent data have determined that the structure of the high pressure $\\epsilon$ phase of solid oxygen consists of clusters composed of four O$_2$ molecules. This finding has opened the question about the nature of the intermolecular interactions within the molecular oxygen tetramer. We use multiconfigurational ab initio calculations to obtain an adequate characterization of the ground singlet state of (O$_2$)$_4$ which is compatible with the non magnetic character of the $\\epsilon$ phase. In contrast to previous suggestions implying chemical bonding, we show that (O$_2$)$_4$ is a van der Waals like cluster where exchange interactions preferentially stabilize the singlet state. However, as the cluster shrinks, there is an extra stabilization due to many-body interactions that yields a significant softening of the repulsive wall. We show that this short range behavior is a key issue for the understanding of the structure of $\\epsilon$-oxygen.

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

2011-01-01

70

Molecular self-assembly on an insulating surface: interplay between substrate templating and intermolecular interactions  

International Nuclear Information System (INIS)

We report on molecular self-assembly of biphenyl-4,4?-dicarboxylic acid (BPDCA) on CaCO3(1 0 1-bar 4) under ultra-high vacuum conditions. Two-dimensional, ordered islands are obtained upon deposition at room temperature, coexisting with a streaky structure that is ascribed to individual, mobile molecules forming a two-dimensional gas-like phase. High-resolution non-contact atomic force microscopy (NC-AFM) images of the molecular islands reveal an ordered inner structure that is dominated by rows of molecules aligned side by side running along the [4261] crystallographic direction. A detailed analysis of these rows exhibits inter-row distances that are multiples of the calcite unit cell dimension along the [0 1 1-bar 0] direction, clearly demonstrating the templating effect of the substrate. Our results indicate that an excellent size match of the molecular structure with respect to the underlying substrate results in an increased binding of the BPDCA molecules to the surface. In between the rows, a different molecular structure is coexisting with the molecules aligning head to tail. This structure is explained by intermolecular hydrogen bond formation very similar to the BPDCA bulk structure. The coexistence of the bulk-like structure with the row structure suggests a close balance of intermolecular and molecule-surface interactions to be responsible for the observed structure formation.

71

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

DEFF Research Database (Denmark)

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 leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Møller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativityon NQC. The same is investigated for d and ?s by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves 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 hand, for the BPPT-based cross coupling of relativity and correlation. For ?ll, 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 129Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe2, are in excellent agreement with the experiment for the first time. © 2007 American Institute of Physics. [DOI: 10.1063/1.2777143

Hanni, Matti; Lantto, Perttu

2007-01-01

72

Manifestation of structure and intermolecular interactions of biologically active brassinosteroids in infrared spectra  

Science.gov (United States)

We have analyzed the IR spectra obtained for steroidal phytohormones 24-epibrassinolide, 24-epicastasterone, 28-homobrassinolide, and 28-homocastasterone. The characteristic frequencies of the stretching vibrations of the hydrocarbon groups CH3, CH2, and CH and also the C=O groups in the spectra of brassinolides are higher than in the spectra of castasterones, which makes it possible to identify them from the IR spectra. Study of the spectra of these brassinosteroids in different media (pressed samples in KBr, films, solutions in CHCl3 and CDCl3) allowed us to establish the presence of intermolecular interactions in which C=O and OH groups, OH-OH groups participate, and also the possible formation of intramolecular hydrogen bonds between the OH groups of the molecules.

Borisevich, N. A.; Skornyakov, I. V.; Khripach, V. A.; Tolstorozhev, G. B.; Zhabinskii, V. N.

2007-09-01

73

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

Science.gov (United States)

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

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

2014-11-01

74

Highly stereoselective asymmetric Pummerer reactions that incorporate intermolecular and intramolecular nonbonded S...O interactions.  

Science.gov (United States)

New chiral sulfoxides (R(S),S)-3, (S(S),S)-3, (R(S),S)-4, and (S(S),S)-4 and known chiral sulfoxides (R(S))-5, (R(S))-6, and (R(S))-7 were synthesized, and the stereochemistry of the new sulfoxides (R(S),S)-3 and (R(S),S)-4 was determined by X-ray crystallographic analysis. In their crystallographic structures, the intramolecular nonbonded S...O close contacts were recognized. Analyses of several sulfoxide complexes including rac-11 with N,N-dimethylacetamide (DMAC) or N-methyl-2-pyrrolidone (NMP) in a MeOH solution utilizing cold-spray ionization mass spectrometry provided, for the first time, direct information for intermolecular nonbonded S...O interactions between sulfoxides and amide (or lactam) in a solution. Highly diastereoselective and enantioselective Pummerer reactions based on the concept of intermolecular and intramolecular nonbonded S...O interactions were performed by treatment of several chiral sulfoxides (R(S), S)-3, (S(S), S)-3, (R(S), S)-4, (S(S), S)-4, (R(S))-5, (R(S))-6, and (R(S))-7 with acetic anhydride and trimethylsilyl triflate (TMSOTf) in DMAC, NMP, N,N-dimethylformamide, and N-formylpiperidine. Mechanistic studies on these facile stereoselective Pummerer reactions revealed the necessity for the amide/TMSOTf complex, such as 26 or 27, to be an efficient activation reagent for Ac(2)O and a trapping reagent for the released acetate ion, and that DMAC and NMP had a positive effect on this highly stereoselective chiral transfer reaction. PMID:16866527

Nagao, Yoshimitsu; Miyamoto, Satoshi; Miyamoto, Motoyuki; Takeshige, Hiroe; Hayashi, Kazuhiko; Sano, Shigeki; Shiro, Motoo; Yamaguchi, Kentaro; Sei, Yoshihisa

2006-08-01

75

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

International Nuclear Information System (INIS)

Highlights: • Ultrasonic, volumetric and spectroscopic properties of 2-CletOH + DMAE/DEAE liquid mixtures were studied. • Results showed the presence of intermolecular hydrogen bonding between the unlike molecules. • H-bonding occurred between hydrogen atom of –OH group of 2-CletOH and oxygen atom of –OH group of DMAE/DEAE. • The strength of intermolecular interactions was found in order: 2-CletOH + DEAE > 2-CletOH + DMAE. - Abstract: The ultrasonic velocity (u) and density (?) of binary mixtures of 2-Chloroethanol (2-CletOH) with 2-Dimethylaminoethanol (DMAE) and 2-Diethylaminoethanol (DEAE) have been measured over the entire concentration range at temperatures 293.15, 303.15 and 313.15 K. The ultrasonic velocity and density data are used to estimate adiabatic compressibility (?S), intermolecular free length (Lf), molar sound velocity (R), molar compressibility (B) and specific acoustic impedance (Z) along with excess values of ultrasonic velocity (uE), adiabatic compressibility (?SE), intermolecular free length (LfE), acoustic impedance (ZE) and molar volume (VmE). The infrared spectra of both of the systems, 2-CletOH + DMAE and 2-CletOH + DEAE, have also been recorded at room temperature (298.15 K). The observed variations of these parameters, with concentration and temperature, are discussed in terms of the intermolecular interactions between the unlike molecules of the binary mixtures

76

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

Energy Technology Data Exchange (ETDEWEB)

Highlights: • Ultrasonic, volumetric and spectroscopic properties of 2-CletOH + DMAE/DEAE liquid mixtures were studied. • Results showed the presence of intermolecular hydrogen bonding between the unlike molecules. • H-bonding occurred between hydrogen atom of –OH group of 2-CletOH and oxygen atom of –OH group of DMAE/DEAE. • The strength of intermolecular interactions was found in order: 2-CletOH + DEAE > 2-CletOH + DMAE. - Abstract: The ultrasonic velocity (u) and density (?) of binary mixtures of 2-Chloroethanol (2-CletOH) with 2-Dimethylaminoethanol (DMAE) and 2-Diethylaminoethanol (DEAE) have been measured over the entire concentration range at temperatures 293.15, 303.15 and 313.15 K. The ultrasonic velocity and density data are used to estimate adiabatic compressibility (?{sub S}), intermolecular free length (L{sub f}), molar sound velocity (R), molar compressibility (B) and specific acoustic impedance (Z) along with excess values of ultrasonic velocity (u{sup E}), adiabatic compressibility (?{sub S}{sup E}), intermolecular free length (L{sub f}{sup E}), acoustic impedance (Z{sup E}) and molar volume (V{sub m}{sup E}). The infrared spectra of both of the systems, 2-CletOH + DMAE and 2-CletOH + DEAE, have also been recorded at room temperature (298.15 K). The observed variations of these parameters, with concentration and temperature, are discussed in terms of the intermolecular interactions between the unlike molecules of the binary mixtures.

Pandey, Puneet Kumar [Material Science Research Laboratory, Department of Physics, University of Lucknow, Lucknow 226 007 (India); Awasthi, Anjali [Department of Physics, BBD University, Lucknow 227 015 (India); Awasthi, Aashees, E-mail: aasheesawasthi@rediffmail.com [Material Science Research Laboratory, Department of Physics, University of Lucknow, Lucknow 226 007 (India)

2013-09-23

77

Intermolecular interaction between a branching ribozyme and associated homing endonuclease mRNA  

DEFF Research Database (Denmark)

Abstract RNA tertiary interactions involving docking of GNRA (N; any base; R; purine) hairpin loops into helical stem structures on other regions of the same RNA are one of the most common RNA tertiary interactions. In this study, we investigated a tertiary association between a GAAA hairpin tetraloop in a small branching ribozyme (DiGIR1) and a receptor motif (HEG P1 motif) present in a hairpin structure on a separate mRNA molecule. DiGIR1 generates a 2', 5' lariat cap at the 5' end of its downstream homing endonuclease mRNA by catalysing a self-cleavage branching reaction at an internal processing site. Upon release, the 5' end of the mRNA forms a distinct hairpin structure termed HEG P1. Our biochemical data, in concert with molecular 3D modelling, provide experimental support for an intermolecular tetraloop receptor interaction between the L9 GAAA in DiGIR1 and a GNRA tetraloop receptor-like motif (UCUAAG-CAAGA) found within the HEG P1. The biological role of this interaction appears to be linked to the homing endonuclease expression by promoting post-cleavage release of the lariat capped mRNA. These findings add to our understanding of how protein-coding genes embedded in nuclear ribosomal DNA are expressed in eukaryotes and controlled by ribozymes.

Birgisdottir, Asa B; Nielsen, Henrik

2011-01-01

78

Spectroscopic studies on weak intermolecular interactions of fluoranthene derivatives with benzene or ethanol in cyclohexane  

International Nuclear Information System (INIS)

Complete text of publication follows. We have published on the spectroscopic study on the formation of a 1:1 molecular complex of fluoranthene (F) with benzene (B) in cyclohexane and estimated the equilibrium constant K(F-B) (0.147 dm3 mol-1 at 298 K), enthalpy change DH(F-B) (-5.9 kJ mol-1) and entropy change DS(F-B) (-36 JK-1mol-1 at 298 K) for this complex formation (S. Enomoto et al., Bull. Chem. Soc. Jpn., 75 (2002) 689-693). In this study, the electronic absorption spectra have been observed for the fluoranthene derivatives in cyclohexane-benzene and/or cyclohexane-ethanol mixed solvents to investigate the weak intermolecular interactions between fluoranthene derivatives and benzene or ethanol. The electronic absorption spectra of 3-aminofluoranthene (AF) in the mixed solvent mentioned above showed isosbestic points with varying B and ethanol (E) concentrations. These observations indicate that AF forms a 1:1 molecular complex with B or E, the K(AF-B) and K(AF-E) values for these complex formations being estimated as 0.146 and 0.647 dm3 mol-1 at 298 K, respectively. Temperature dependence of K(AF-B) and K(AF-E) yielded ?H(AF-B) and ?H(AF-E) values of -6.3 and -14.2 kJ mol-1, respectively, ?S(AF-B) and ?S(AF-E) values being respectively calculated as -40 and -51 JK-1mol-1 at 298 K. Applying similar experimental and calculational procedures to 3-nitrofd calculational procedures to 3-nitrofluoranthene (NF) in cyclohexane-B mixed solvent, K(NF-B), ?H(NF-B) and ?S(NF-B) values were estimated as 0.064 dm3 mol-1 at 298 K, -14.6 kJ mol-1 and -72 JK-1 mol1 at 298 K, respectively, for the 1:1 molecular complex formation of NF with B. It is interesting to note that the amino group has almost no effect on the stability of F-B molecular complex since K(AF-B) is comparable to K(F-B) value. It is, further, noted that AF-E and NF-B complexes are enthalpically easier and entropically harder to be formed, respectively, than AF-B one. Assuming that the dispersion energy involved in ?H(NF-B) is the same in magnitude as ?H(F-B) which is considered to be purely dispersion energy, the induction energy contributed to ?H(NF-B) is calculated as -8.7 kJ mol-1. Concerning the conformations of AF-B and NF-B molecular complexes, both the ab initio and PPP calculations support the sandwich- or parallel-type.

79

Effects of Weak Intermolecular Interactions on the Molecular Isomerism of Tricobalt Metal Chains  

International Nuclear Information System (INIS)

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 tinteractions, 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 interactions with the terminal chlorine atom Cl(1). The Co(3) atom has a relatively high occupancy of the dx2-y2 orbital and a relatively low occupancy of the dxy orbital confirming that these orbitals are involved in the spin crossover process and predominantly responsible for the observed variation in bond lengths with temperature.

80

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

Science.gov (United States)

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

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

2014-01-01

 
 
 
 
81

Molecular complex consisting of two typical external medicines: intermolecular interaction between indomethacin and lidocaine.  

Science.gov (United States)

The molecular complex formed between indomethacin (IDM) and lidocaine (LDC), which are typical external medicines, was studied. A thermal analysis, microscopic study and phase solubility technique suggested intermolecular interaction between IDM and LDC. The phase solubility profiles with IDM and LDC were classified as A(L)-type, indicating the formation of a 1 : 1 stoichiometric molecular complex. The apparent stability constant (K(S)), calculated from the slope and the intercept, was 4478.9 M(-1). A molecular ion peak was detected at 592.2 (m/z) from fast-atom bombardment-MS measurements, which was in accordance with the sum of the molecular weight for IDM (M(W): 357.81) and LDC (M(W): 234.38). The changes of IR spectra in the C=O stretching region showed that each intact hydrogen bond network was collapsed in the IDM-LDC system and strong interaction between IDM and LDC formed after their kneading. From the (1)H-NMR analyses, it was estimated that the dominant interactive site was the IDM carboxylic acid group which associated with the LDC diethyl amino group non-covalently. PMID:17473482

Umeda, Yukiko; Fukami, Toshiro; Furuishi, Takayuki; Suzuki, Toyofumi; Makimura, Mizue; Tomono, Kazuo

2007-05-01

82

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

Science.gov (United States)

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

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

2013-09-01

83

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

Science.gov (United States)

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

Osipov, M A; Gorkunov, M V

2008-03-01

84

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

Science.gov (United States)

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

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

2014-09-01

85

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

Science.gov (United States)

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

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

2004-12-01

86

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

Science.gov (United States)

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

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

2013-02-01

87

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

Directory of Open Access Journals (Sweden)

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

Michael Roos

2011-07-01

88

Intermolecular Attractions  

Science.gov (United States)

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

The Concord Consortium

2011-12-11

89

Intermolecular Interactions in Ternary Glycerol–Sample–H2O : Towards Understanding the Hofmeister Series (V)  

DEFF Research Database (Denmark)

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-butanol (TBA), 1-propanol (1P), urea (UR), NaF, NaCl, NaBr, NaI, and NaSCN were used. It was found that hydrophobes (TBA and 1P) reduce the values of HGly-GlyEHEGly--Gly considerably, but a hydrophile (UR) had very little effect on HGly-GlyEHEGly--Gly. The results with Na salts indicated that there have very 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 hydrophilic. These observations hint that whatever effect each individual ion has on H2O, it is sensitive only to hydrophobes (such as 1P) but not to hydrophiles (such as Gly). This may have an important bearing towards understanding the Hofmeister series, since biopolymers are amphiphilic and their surfaces are covered by hydrophobic as well as hydrophilic parts.

Westh, Peter; Rasmussen, Erik Lumby

2011-01-01

90

Theory of intermolecular forces  

CERN Document Server

Theory of Intermolecular Forces deals with the exposition of the principles and techniques of the theory of intermolecular forces. The text focuses on the basic theory and surveys other aspects, with particular attention to relevant experiments. The initial chapters introduce the reader to the history of intermolecular forces. Succeeding chapters present topics on short, intermediate, and long range atomic interactions; properties of Coulomb interactions; shape-dependent forces between molecules; and physical adsorption. The book will be of good use to experts and students of quantum mechanics

Margenau, H; Ter Haar, D

1971-01-01

91

Investigations on stabilities and intermolecular interactions of different naphthalene derivatives dimers by using B3LYP and M06-2X density functional calculations  

Science.gov (United States)

In this paper, the stabilities and hydrogen bond interactions of 4-chloro-1-naphthol, 1-hydrox-ynaphthalene and 1,4-dihydroxynaphthalene dimers have been theoretically investigated by means of study on binding energies with nonlocal hybrid three-parameter Lee-Yang-Parr, B3LYP, and M06-class functional calculations. Calculations on dimers aim to provide as a test of the efficacy of M06 calculations for intermolecular interaction calculations and more strongly bound systems. For hydroxyl- and halo-substituted derivatives of naphthalene, total electronic energies, their correction for the zero point vibrational energies with some calculated thermodynamic properties and their relative differences are together in order to discuss the rotamer structures. Static (hyper) polarizabilities and the electric dipole moments, frontier molecular orbital energy gaps and the relationships between them have been interpreted. Generally, they are seen that the calculated geometric parameters and spectral results were in a good agreement with the corresponding experimental data.

Karakaya, M.; Çiçek, A.; Ucun, F.; Yildiz, M.

2014-12-01

92

Intermolecular energy transfer in the presence of dispersing and absorbing media  

CERN Document Server

By making use of the Green function concept of quantization of the electromagnetic field in Kramers--Kronig consistent media, a rigorous quantum mechanical derivation of the rate of intermolecular energy transfer in the presence of arbitrarily shaped, dispersing, and absorbing material bodies is given. Applications to bulk material, multi-slab planar structures, and microspheres are studied. It is shown that when the two molecules are near a planar interface, then surface-guided waves can strongly affect the energy transfer and essentially modify both the (F\\"{o}rster) short-range $R^{-6}$ dependence of the transfer rate and the long-range $R^{-2}$ dependence, which are typically observed in free space. In particular, enhancement (inhibition) of energy transfer can be accompanied by inhibition (enhancement) of donor decay. Results for four- and five-layered planar structures are given and compared with experimental results. Finally, the energy transfer between two molecules located at diametrically opposite p...

Dung, H T; Welsch, D G; Dung, Ho Trung; Kn\\"{o}ll, Ludwig; Welsch, Dirk-Gunnar

2002-01-01

93

Intermolecular effect in molecular electronics.  

Science.gov (United States)

We investigate the effects of lateral interactions on the conductance of two molecules connected in parallel to semi-infinite leads. The method we use combines a Green function approach to quantum transport with density functional theory for the electronic properties. The system, modeled after a self-assembled monolayer, consists of benzylmercaptane molecules sandwiched between gold electrodes. We find that the conductance increases when intermolecular interaction comes into play. The source of this increase is the indirect interaction through the gold substrate rather than direct molecule-molecule interaction. A striking resonance is produced only 0.3 eV above the Fermi energy. PMID:15740279

Liu, Rui; Ke, San-Huang; Baranger, Harold U; Yang, Weitao

2005-01-22

94

Intermolecular Effect in Molecular Electronics  

CERN Document Server

We investigate the effects of lateral interactions on the conductance of two molecules connected in parallel to semi-infinite leads. The method we use combines a Green function approach to quantum transport with density functional theory for the electronic properties. The system, modeled after a self-assembled monolayer, consists of benzylmercaptane molecules sandwiched between gold electrodes. We find that the conductance increases when intermolecular interaction comes into play. The source of this increase is the indirect interaction through the gold substrate rather than direct molecule-molecule interaction. A striking resonance is produced only 0.3 eV above the Fermi energy.

Liu, R; Baranger, H U; Yang, W; Liu, Rui; Ke, San-Huang; Baranger, Harold U.; Yang, Weitao

2005-01-01

95

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

Science.gov (United States)

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

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

2004-07-22

96

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

Science.gov (United States)

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

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

2004-07-01

97

THE INTERACTION OF PARAMAGNETIC RELAXATION REAGENTS WITH INTRA- AND INTERMOLECULAR HYDROGEN BONDED PHENOLS  

Science.gov (United States)

Intermolecular electron-nuclear 13-C relaxation times (T(1)sup e's) from solutions containing the paramagnetic relaxation reagent (PARR), Cr(acac)3, used in conjunction with 13-C T(1)'s in diamagnetic solutions (intramolecular 13-C - (1)H dipolar T(1)'s) provide a significant inc...

98

Intermolecular resonance energy transfer in the presence of a dielectric cylinder  

International Nuclear Information System (INIS)

Using a Green's tensor method, we investigate the rate of resonance electronic energy transfer between two molecules near a dielectric cylinder. Both the case of a real and frequency-independent dielectric constant ? and the case of a Drude-Lorentz model for ?(?) are considered, the latter case including dispersion and absorption. If the donor is placed at a fixed position near the cylinder, we find that the energy transfer rate to the acceptor is enhanced compared to its vacuum value in a number of discrete hotspots, centered at the cylinder's surface. In the absence of dispersion and absorption the rate of energy transfer may be enhanced at most a few times. On the other hand, for the Drude-Lorentz model the enhancement may be huge (up to 106) and the hotspots are sharply localized at the surface. We show that these observations can be explained from the fact that in the resonance region of the Drude-Lorentz dielectric surface plasmons occur, which play the dominant role in transferring the electronic energy between the donor and the acceptor. The dependence of the energy transfer rate on the molecular transition frequency is investigated as well. For small intermolecular distances, the cylinder hardly affects the transfer rate, independent of frequency. For larger distances, the frequency dependence is quite strong, in particular in the stop-gap region. The role of the intermolecular distance in the frequency dependence may be explained qualitatively endence may be explained qualitatively using Heisenberg's uncertainty principle to calculate the spread in the frequencies of the intermediate photons.

99

Intra- and intermolecular interactions in small bioactive molecules: cooperative features from experimental and theoretical charge-density analysis.  

Science.gov (United States)

The topological features of the charge densities, rho(r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1H)-one], cytosine [4-aminopyrimidin-2(1H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of 'Atoms In Molecules'. The roles of interactions such as C-H...O, C-H...S, C-H...pi and pi...pi have been investigated quantitatively in the presence of strong hydrogen bonds such as O-H...O, N-H...O and N-H...S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S...S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug-receptor recognition. PMID:16840811

Munshi, Parthapratim; Guru Row, Tayur N

2006-08-01

100

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

Science.gov (United States)

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

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

2005-04-22

 
 
 
 
101

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

Science.gov (United States)

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

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

2009-04-01

102

Molecular packing and intermolecular interactions in two structural polymorphs of N-palmitoylethanolamine, a type 2 cannabinoid receptor agonist.  

Science.gov (United States)

The molecular structure, packing properties, and intermolecular interactions of two structural polymorphs of N-palmitoylethanolamine (NPEA) have been determined by single-crystal X-ray diffraction. Polymorphs alpha and beta crystallized in monoclinic space group P2(1)/c and orthorhombic space group Pbca, respectively. In both polymorphs, NPEA molecules are organized in a tail-to-tail manner, resembling a bilayer membrane. Although the molecular packing in polymorph alpha is similar to that in N-myristoylethanolamine and N-stearoylethanolamine, polymorph beta is a new form. The acyl chains in both polymorphs are tilted by approximately 35 degrees with respect to the bilayer normal, with their hydrocarbon moieties packed in an orthorhombic subcell. In both structures, the hydroxy group of NPEA forms two hydrogen bonds with the hydroxy groups of molecules in the opposite leaflet, resulting in extended, zig-zag type H-bonded networks along the b-axis in polymorph alpha and along the a-axis in polymorph beta. Additionally, the amide N-H and carbonyl groups of adjacent molecules are involved in N-H...O hydrogen bonds that connect adjacent molecules along the b-axis and a-axis, respectively, in alpha and beta. Whereas in polymorph alpha the L-shaped NPEA molecules in opposite layers are arranged to yield a Z-like organization, in polymorph beta one of the two NPEA molecules is rotated 180 degrees , leading to a W-like arrangement. Lattice energy calculations indicate that polymorph alpha is more stable than polymorph beta by approximately 2.65 kcal/mol. PMID:16609146

Kamlekar, Ravi Kanth; Swamy, Musti J

2006-07-01

103

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

Science.gov (United States)

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

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

2014-10-13

104

Lack of evidence for intermolecular epistatic interactions between adiponectin and resistin gene polymorphisms in Malaysian male subjects  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english Epistasis (gene-gene interaction) is a ubiquitous component of the genetic architecture of complex traits such as susceptibility to common human diseases. Given the strong negative correlation between circulating adiponectin and resistin levels, the potential intermolecular epistatic interactions be [...] tween ADIPOQ (SNP+45T > G, SNP+276G > T, SNP+639T > C and SNP+1212A > G) and RETN (SNP-420C > G and SNP+299G > A) gene polymorphisms in the genetic risk underlying type 2 diabetes (T2DM) and metabolic syndrome (MS) were assessed. The potential mutual influence of the ADIPOQ and RETN genes on their adipokine levels was also examined. The rare homozygous genotype (risk alleles) of SNP-420C > G at the RETN locus tended to be co-inherited together with the common homozygous genotypes (protective alleles) of SNP+639T > C and SNP+1212A > G at the ADIPOQ locus. Despite the close structural relationship between the ADIPOQ and RETN genes, there was no evidence of an intermolecular epistatic interaction between these genes. There was also no reciprocal effect of the ADIPOQ and RETN genes on their adipokine levels, i.e., ADIPOQ did not affect resistin levels nor did RETN affect adiponectin levels. The possible influence of the ADIPOQ gene on RETN expression warrants further investigation.

Cia-Hin, Lau; Sekaran, Muniandy.

105

Lack of evidence for intermolecular epistatic interactions between adiponectin and resistin gene polymorphisms in Malaysian male subjects  

Directory of Open Access Journals (Sweden)

Full Text Available Epistasis (gene-gene interaction is a ubiquitous component of the genetic architecture of complex traits such as susceptibility to common human diseases. Given the strong negative correlation between circulating adiponectin and resistin levels, the potential intermolecular epistatic interactions between ADIPOQ (SNP+45T > G, SNP+276G > T, SNP+639T > C and SNP+1212A > G and RETN (SNP-420C > G and SNP+299G > A gene polymorphisms in the genetic risk underlying type 2 diabetes (T2DM and metabolic syndrome (MS were assessed. The potential mutual influence of the ADIPOQ and RETN genes on their adipokine levels was also examined. The rare homozygous genotype (risk alleles of SNP-420C > G at the RETN locus tended to be co-inherited together with the common homozygous genotypes (protective alleles of SNP+639T > C and SNP+1212A > G at the ADIPOQ locus. Despite the close structural relationship between the ADIPOQ and RETN genes, there was no evidence of an intermolecular epistatic interaction between these genes. There was also no reciprocal effect of the ADIPOQ and RETN genes on their adipokine levels, i.e., ADIPOQ did not affect resistin levels nor did RETN affect adiponectin levels. The possible influence of the ADIPOQ gene on RETN expression warrants further investigation.

Cia-Hin Lau

2012-01-01

106

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

Science.gov (United States)

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

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

2014-01-01

107

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

Science.gov (United States)

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

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

2014-10-01

108

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

Science.gov (United States)

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

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

2014-12-01

109

A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Kr-H2O complex  

Science.gov (United States)

We report a new three-dimensional ab initio intermolecular potential energy surface for the Kr-H2O complex with the H2O monomer fixed at its experimental averaged structure. Using the supermolecular approach, the intermolecular potential energies were evaluated at the coupled-cluster singles and doubles level with noniterative inclusion of connected triples with the full counterpoise correction for the basis set superposition error and a large basis set including bond functions. The global minimum corresponding to a planar H-bond configuration was located at the intermolecular distance of 3.82 Å with a well depth of 169.98 cm-1. In addition, two first-order and one second-order saddle points were also identified. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to calculate the rovibrational energy levels for 16 isotopic species of the Kr-H2O complexes. The rotational transition frequencies, structure parameters, and nuclear quadrupole coupling constants were also determined for the ground and first intermolecular vibrational excited states and are all in good agreement with the available experimental values.

Lei, Jinping; Zhou, Yanzi; Xie, Daiqian; Zhu, Hua

2012-12-01

110

A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Kr-H2O complex.  

Science.gov (United States)

We report a new three-dimensional ab initio intermolecular potential energy surface for the Kr-H(2)O complex with the H(2)O monomer fixed at its experimental averaged structure. Using the supermolecular approach, the intermolecular potential energies were evaluated at the coupled-cluster singles and doubles level with noniterative inclusion of connected triples with the full counterpoise correction for the basis set superposition error and a large basis set including bond functions. The global minimum corresponding to a planar H-bond configuration was located at the intermolecular distance of 3.82 A? with a well depth of 169.98 cm(-1). In addition, two first-order and one second-order saddle points were also identified. The combined radial discrete variable representation?angular finite basis representation method and the Lanczos algorithm were employed to calculate the rovibrational energy levels for 16 isotopic species of the Kr-H(2)O complexes. The rotational transition frequencies, structure parameters, and nuclear quadrupole coupling constants were also determined for the ground and first intermolecular vibrational excited states and are all in good agreement with the available experimental values. PMID:23249010

Lei, Jinping; Zhou, Yanzi; Xie, Daiqian; Zhu, Hua

2012-12-14

111

Quantum electrodynamics with nonrelativistic sources. V. Electromagnetic field correlations and intermolecular interactions between molecules in either ground or excited states  

International Nuclear Information System (INIS)

Spatial correlations between electromagnetic fields arising from neutral sources with electric-dipole transition moments are calculated using nonrelativistic quantum electrodynamics in the multipolar formalism. Expressions for electric-electric, magnetic-magnetic, and electric-magnetic correlation functions at two points r and r' are given for a source molecule in either a ground or an excited state. In contrast to the electric-electric and magnetic-magnetic cases there are no electric-magnetic correlations for a ground-state molecule. For an excited molecule the downward transitions contribute additional terms which have modulating factors depending on (r-r')/?. From these correlation functions electric and magnetic energy densities are found by setting r=r'. These energy densities are then used in a response formalism to calculate intermolecular energy shifts. In the case of two ground-state molecules this leads to the Casimir-Polder potential. However, for a pair of molecules, one or both excited, there are additional terms arising from downward transitions. An important feature of these energies is that they exhibit an R-2 dependence for large intermolecular separations R. This dependence is interpreted in terms of the Poynting vector, which itself can be obtained by setting r=r' in the electric-magnetic correlation function

112

Determination of the intermolecular potential energy surface for (HCl)2 from vibration-rotation-tunneling spectra  

Science.gov (United States)

An accurate and detailed semiempirical intermolecular potential energy surface for (HCl)2 has been determined by a direct nonlinear least-squares fit to 33 microwave, far-infrared and near-infrared spectroscopic quantities using the analytical potential model of Bunker et al. [J. Mol. Spectrosc. 146, 200 (1991)] and a rigorous four-dimensional dynamical method (described in the accompanying paper). The global minimum (De=-692 cm-1) is located near the hydrogen-bonded L-shaped geometry (R=3.746 Å, ?1=9°, ?2=89.8°, and ?=180°). The marked influence of anisotropic repulsive forces is evidenced in the radial dependence of the donor-acceptor interchange tunneling pathway. The minimum energy pathway in this low barrier (48 cm-1) process involves a contraction of 0.1 Å in the center of mass distance (R) at the C2h symmetry barrier position. The new surface is much more accurate than either the ab initio formulation of Bunker et al. or a previous semiempirical surface [J. Chem. Phys. 78, 6841 (1983)].

Elrod, M. J.; Saykally, R. J.

1995-07-01

113

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

International Nuclear Information System (INIS)

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–Chauddhri, Tamura–Kurata, Auslander and McAllister) have also been used to fit the viscosity values

114

Further analysis and comparative study of intermolecular interactions using dimers from the S22 database  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Accurate MP2 and CCSD(T) complete basis set (CBS) interaction energy curves (14 points for each curve) have been obtained for 20 of the dimers reported in the S22 set and analytical Morse curves have been fitted that can be used in developing updated density functional theory (DFT) and force field models. The magnitude and the effect of the basis set superposition error (BSSE) were carefully investigated. We found that going up to aug-cc-pVDZ and aug-cc-pVTZ basis sets is enough to obtain acc...

Molnar, Laszlo Fusti; He, Xiao; Wang, Bing; Merz, Kenneth M.

2009-01-01

115

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

International Nuclear Information System (INIS)

The results of X-ray structural studies of liquid chloroanisole C6H4OCH3Cl and 10% solutions of chloroanisole in 1,4-dimethylbenzene C8H10 are presented. It is the first paper on an X-ray diffraction study of the liquid solutions of chloroanisole. The X-ray measurements were made at 293 K for the scattering angle range 2? varying from 6° to 120°. Averaged scattered X-ray angular distributions I¯(S) were determined. The angular distributions of the intensity of X-ray scattered by 10% solutions of chloroanisole in 1,4-dimethylbenzene were compared to the angular distributions obtained for liquid ortho-, meta- and para-chloroanisole. The differential radial distribution functions of electron density 4?r2?j,knK¯j[?k(r)??0] were numerically found using the Fourier analysis from a modified Warren, Krutter and Morningstar equation. To the maxima of DRDFs, interatomic and intermolecular distances were assigned. The use of short-wave radiation from an X-ray tube with a molybdenum anode permitted determination of the spheres of intermolecular ordering in the studied liquids and their solutions. The experimental results were used to plot models of the most highly probable mutual disposition of the molecules in liquid chloroanisole and their solutions. The benzene rings of two molecules are situated in parallel plane what results in antiparallel setting of the dipole moments of the chloroanisole molecules. X-ray structural analysis was applied to determine the packing coefficients of chloroanisole molecules. The results obtained in this paper confirm the specific structural properties of the solutions studied. - Highlights: • The results of X-ray structural studies of liquid chloroanisole and 10% solutions of chloroanisole in 1,4-dimethylbenzene are presented. • There was existence of spheres of intermolecular ordering in the studied solutions. • Measurements were carried out at a temperature of 293 K. • The presence of short-range ordering reaching about 20 Å in the molecular liquids studied has been proved. • The packing coefficient of the chloroanisoles accordingly are about 63%

116

Tuning intermolecular interactions to enhance solid-state nanopore force spectroscopy  

Science.gov (United States)

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

Foun, Elaine

117

Intermolecular C–H?O interactions in cyclopentanone: An inelastic neutron scattering study  

International Nuclear Information System (INIS)

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

118

Intermolecular O-H...O and C-H...?(C5H5), and intramolecular C-H...O interactions in 2-(ferrocenyl)thiophene-3-carboxylic acid  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The title compound, [Fe(C?H?)(C??H?O?S)], an important precursor en route to organometallic donor-?-acceptor systems, forms dimers in the solid state through cyclic intermolecular carboxylic acid O-H...O hydrogen bonds, graph set R²?(8) [O...O 2.661 (2) Å and O-H...O 175°]. Intermolecular Ccp-H...?cp interactions between the unsubstituted cyclopentadienyl (Cp) rings and Cthiazole-H...?cp interactions link neighbouring molecules into a three-dimensional network [C...Cg 3....

Gallagher, John F.; Hudson, Richard D. A.; Manning, Anthony R.

2001-01-01

119

A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Ne-H2S complex  

Science.gov (United States)

We report a new three-dimensional ab initio intermolecular potential energy surface for the Ne-H2S complex with H2S monomer fixed at its experimental average structure. Using the supermolecular approach, the intermolecular potential energies were evaluated at CCSD(T) (coupled cluster with single and double and perturbative triple excitations) level with large basis sets including bond functions. The full counterpoise procedure was employed to correct the basis set superposition error. The planar T-shaped global minimum is located at the intermolecular distance of 3.51 Å with a well depth of 71.57 cm-1. An additional planar local minimum was found to be separated from the global minimum with an energy barrier of 23.11 cm-1. In addition, two first-order and one second-order saddle points were also located. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to evaluate the rovibrational energy levels for eight isotopic species of the Ne-H2S complexes. The rotational transition frequencies for the eight isotopomers were also determined for the ground and first vibrational excited states, which are all in very good agreement with the available experimental values.

Lei, Jinping; Xiao, Mengying; Zhou, Yanzi; Xie, Daiqian

2012-06-01

120

A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Ne-H2S complex.  

Science.gov (United States)

We report a new three-dimensional ab initio intermolecular potential energy surface for the Ne-H(2)S complex with H(2)S monomer fixed at its experimental average structure. Using the supermolecular approach, the intermolecular potential energies were evaluated at CCSD(T) (coupled cluster with single and double and perturbative triple excitations) level with large basis sets including bond functions. The full counterpoise procedure was employed to correct the basis set superposition error. The planar T-shaped global minimum is located at the intermolecular distance of 3.51 Å with a well depth of 71.57 cm(-1). An additional planar local minimum was found to be separated from the global minimum with an energy barrier of 23.11 cm(-1). In addition, two first-order and one second-order saddle points were also located. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to evaluate the rovibrational energy levels for eight isotopic species of the Ne-H(2)S complexes. The rotational transition frequencies for the eight isotopomers were also determined for the ground and first vibrational excited states, which are all in very good agreement with the available experimental values. PMID:22697543

Lei, Jinping; Xiao, Mengying; Zhou, Yanzi; Xie, Daiqian

2012-06-01

 
 
 
 
121

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

Science.gov (United States)

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

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

2014-12-01

122

Control of Hap1-DNA site recognition through the interplay of multiple distinct intermolecular interactions.  

Science.gov (United States)

Hap1 belongs to the Zn(2)Cys(6) zinc binuclear cluster family of transcription factors that typically bind as dimers to symmetric DNA sites containing two CGG triplets separated by spacer DNA. The cluster domain binds CGG while an adjoining C-terminal linker and dimerization helix specifies the length of spacer DNA recognized. Hap1 is unusual in binding a direct repeat of CGG triplets, in contacting a TA in the spacer DNA, and in making direct dimer contacts between its cluster domains. Binding of Hap1 fragments to different DNA sites was tested to determine how these interactions control Hap1-DNA recognition. The spacer TA contacts were found to facilitate monomer binding of Hap1 to a single CGG. When the spacer-binding residues were deleted, binding was still specific for the direct repeat but was much weaker and appeared to require dimerization. When the dimerization helix and all subsequent C-terminal residues were deleted, the remaining linker, cluster domain, and spacer-binding residues still dimerized on DNA. The energy of this dimerization was comparable to that of the Hap1-spacer TA interaction. Moving the TA from the spacer to a position following the second CGG maintained Hap1 monomer binding but greatly weakened dimerization. This suggested that binding a TA after the second CGG triplet required a geometry that impaired dimerization with a Hap1 molecule on the first CGG. The geometric restraints for optimal TA binding and dimerization thus drive Hap1 selectivity for CGG direct repeat sites that contain an asymmetrically positioned spacer TA following the first CGG triplet. PMID:15504044

Wang, Lee L; Denman, Inga; Junker, Matthew

2004-11-01

123

Intermolecular interactions and thermodynamic properties of 3,6-diamino-1,2,4,5-tetrazine-1,4-dioxide dimers: A density functional theoretical study  

Scientific Electronic Library Online (English)

Full Text Available SciELO South Africa | Language: English Abstract in english Three fully optimized structures of 3,6-diamino-1,2,4,5-tetrazine-1,4-dioxide (LAX-112) dimers have been obtained with the density functional theory (DFT) method at the B3LYP/6-311++G level. Vibrational frequency calculations were carried out to ascertain that each structure is a minimum (no imagina [...] ry frequencies). The intermolecular interaction energy is calculated with the basis set superposition error (BSSE) correction and zero point energy (ZPE) correction. The greatest corrected binding energy among the three dimers is -42.38 kJ mol-1. The charge redistribution mainly occurs on the adjacent O(N)......H atoms between submolecules and the charge transfer between two subsystems is very small. Natural bond orbital (NBO) analysis was performed to reveal the origin of the interaction. Based on the vibrational analysis, the standard thermodynamic functions (heat capacities (cºp), entropies (S°m) and enthalpies (H°m)) and the changes of thermodynamic properties from the monomer to dimer with the temperature ranging from 200.00 K to 800.00 K have been obtained using statistical thermodynamics. The results show that the strong hydrogen bonds dominantly contribute to the dimers, while the bonding energies are not only determined by the hydrogen bonding. The dimerization process of dimer II can occur spontaneously at room temperature.

Ning Ning, Zhao; Ya Ling, Zhao; Yin, Hu; Hai Xia, Ma; Feng Qi, Zhao; Ji Rong, Song.

2013-08-01

124

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

Science.gov (United States)

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

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

2013-01-15

125

Quantitative tomographic imaging of intermolecular FRET in small animals  

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Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a m...

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

2012-01-01

126

Multibody effects in intermolecular interactions and reaction pathways for catalytic processes. Part II the contributions of Sidonio Castillo  

Scientific Electronic Library Online (English)

Full Text Available SciELO Mexico | Language: English Abstract in spanish Aquí continuaremos la revisión del trabajo de Octavio Novaro y sus colaboradores en los importantes campos de la no aditividad de las interacciones intermoleculares y de la catálisis, enfatizando las contribuciones de Sidonio Castillo que resultaron altamente útiles en este esfuerzo conjunto, antes [...] de su prematuro fallecimiento. Sus primeros trabajos, con reconocidos científico polacos en los trímeros de metáno y amoniaco y con coautores ingleses en trimeros y tetrameros de fósforo y nitrógeno, serán presentados primero, seguidos de sus estudiós sobre la activación catalítica de moléculas de metáno, silano y germano (de alto potencial en aplicaciónes valiosas). Sus primeros trabajos en catálisis formaron parte de su tesis doctoral dirigida por O. Novaro y los últimos fueron consecuencia de las tesis doctorales que el Dr. Castillo dirigió a los otros dos coautores de esta revisión. Esta labor fue desgraciadamente interrumpida por la muerte de Sidonio. Así concluyó su corta pero brillante carrera. Abstract in english We here continue the review on the work of Octavio Novaro and collaborators in the important field of nonadditivity of intermolecular interactions and catalysis, with special interest in the work that Sidonio Castillo contributed to this effort before his demise. His early work with Polish coauthors [...] on methane and ammonia trimers and with British coauthors on N3, P3, N4 and P4 are highlighted. Then our focus will shift mainly to his work on the activation of methane, silane and germane starting with his Ph.D. thesis under O. Novaro and ending in his last papers with the present authors which marked the end of his short but brilliant career.

O., Novaro; J.H., Pacheco-Sánchez; H., Luna.

2009-10-01

127

Determination of stepsize parameters for intermolecular vibrational energy transfer: Progress report, May 1, 1987-April 30, 1988  

International Nuclear Information System (INIS)

Intermolecular vibrational energy transfer for highly excited polyatomic molecules is involved in any mechanism in which excitation energy is required (pyrolysis) or in which energy must be removed from a hot source (cooling). The average energy removed per collision, , is a useful quantity to compare efficiency for energy transfer. The objectives of this work are: to determine the dependence of on excitation energy and on the molecular complexity (number of vibrational modes) of substrate and deactivator; to assess the importance of intermolecular attractions (complex formation) on vibrational energy transfer; to obtain detailed information on the energy distribution after collision and to evaluate the importance of on high-temperature unimolecular reactions. This information will be obtained by monitoring the time dependence of the infrared emission, ultraviolet absorption, refractive index and pressure. The results from these complementary techniques will be benchmarked with values from previous studies on the relaxation of chemically activated alkyl and fluoroalkyl radicals. Trajectory calculations simulating energy transfer are being performed for ''generic'' substrate/deactivator pairs to provide additional details and insight on the important parameters. Model calculations are also being performed to determine the feasibility of obtaining information from experimental data for high-temperature unimolecular reactions

128

12C/13C and H/D vapor pressure isotope effects of fluoroform: intermolecular interactions in liquid fluoroform  

International Nuclear Information System (INIS)

A precision cryostat of the Bigeleisen-Brooks-Ribnikar-Ishida (BBIR) type with associated vacuum systems has been constructed and the appropriate temperature/pressure measurement and control systems designed and implemented. Various improvements in the cryostat design were incorporated in order to facilitate the assembly and repair processes. A major design change involved the incorporation of a digital stand alone computer to control cryostat operations. This apparatus was used to measure the 12C/13C and H/D Vapor Pressure Isotope Effects of Fluoroform. Analysis of the measured VPIE results, in light of existing experimental data and theories, has demonstrated the need of a temperature dependent liquid force field, specifically a temperature-dependent interaction force constant between the C-H stretching motion and translational motion in the direction of the figure axis of CHF3. This result is consistent with the observed spectroscopic data and vibrational and configurational models of fluoroform dimers. The intermolecular interaction is believed to be a weak hydrogen-bond in nature

129

New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular receptors. Here, we propose a new solvation free energy function through the improvement of the solvent-contact model, and test its applicability in estimating the solvation free energies of organic molecules with varying sizes and shapes. This new solvation free energy function is constructed by combining the existing solute-solvent interaction term with the self-solvation term that reflects the effects of intramolecular interactions on solvation. Four kinds of atomic parameters should be determined in this solvation model: atomic fragmental volume, maximum atomic occupancy, atomic solvation, and atomic self-solvation parameters. All of these parameters for total 37 atom types are optimized by the operation of a standard genetic algorithm in such a way to minimize the difference between the experimental solvation free energies and those calculated by the solvation free energy function for 362 organic molecules. The solvation free energies estimated from the new solvation model compare well with the experimental results with the associated squared correlation coefficients of 0.88 and 0.85 for training and test sets, respectively. The present solvation model is thus expected to be useful for estimating the solvation free energies of organic molecules.

Choi Hwanho

2013-02-01

130

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

International Nuclear Information System (INIS)

Highlights: ? The carbonyl overtone of acetone clusters is observed by IR-VUV spectroscopy. ? Acetone molecules in the dimer are stacked with an antiparallel way. ? The structure of the acetone trimer and the tetramer are the cyclic structures. ? The carbonyl groups would interact with the methyl groups in acetone clusters. ? These weak interactions are further confirmed by H/D substitution experiment. -- Abstract: Size-selected IR–VUV spectroscopy is employed to detect vibrational characteristics in the region 2850 ? 3550 cm?1 of neutral acetone and its clusters (CH3COCH3)n (n = 1–4). Features around 3440 cm?1 in the spectra of acetone monomer and its clusters are assigned to the carbonyl stretch (CO) overtone. These features red-shift from 3455 to 3433 cm?1 as the size of the clusters increases from the monomer to the tetramer. Based on calculations, the experimental IR spectra in the C=O overtone region suggest that the dominant structures for the acetone trimer and tetramer should be cyclic in the supersonic expansion sample. This study also suggests that the carbonyl groups interact with the methyl groups in the acetone clusters. These weak interactions are further confirmed by the use of deuterium substitution.

131

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

Energy Technology Data Exchange (ETDEWEB)

Highlights: Black-Right-Pointing-Pointer The carbonyl overtone of acetone clusters is observed by IR-VUV spectroscopy. Black-Right-Pointing-Pointer Acetone molecules in the dimer are stacked with an antiparallel way. Black-Right-Pointing-Pointer The structure of the acetone trimer and the tetramer are the cyclic structures. Black-Right-Pointing-Pointer The carbonyl groups would interact with the methyl groups in acetone clusters. Black-Right-Pointing-Pointer These weak interactions are further confirmed by H/D substitution experiment. -- Abstract: Size-selected IR-VUV spectroscopy is employed to detect vibrational characteristics in the region 2850 {approx} 3550 cm{sup -1} of neutral acetone and its clusters (CH{sub 3}COCH{sub 3}){sub n} (n = 1-4). Features around 3440 cm{sup -1} in the spectra of acetone monomer and its clusters are assigned to the carbonyl stretch (CO) overtone. These features red-shift from 3455 to 3433 cm{sup -1} as the size of the clusters increases from the monomer to the tetramer. Based on calculations, the experimental IR spectra in the C=O overtone region suggest that the dominant structures for the acetone trimer and tetramer should be cyclic in the supersonic expansion sample. This study also suggests that the carbonyl groups interact with the methyl groups in the acetone clusters. These weak interactions are further confirmed by the use of deuterium substitution.

Guan, Jiwen [MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631 (China); Hu, Yongjun, E-mail: yjhu@scnu.edu.cn [MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631 (China); Xie, Min [MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631 (China); Bernstein, Elliot R. [Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 (United States)

2012-09-11

132

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

Science.gov (United States)

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

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

2014-12-01

133

A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Ar-H2S complex  

Science.gov (United States)

We report a reliable three-dimensional ab initio intermolecular potential energy surface for the Ar-H2S complex with H2S monomer fixed at its experimental average structure. The potential energies were evaluated using the supermolecular approach at the coupled-cluster level with a large basis set including bond functions. The full counterpoise procedure was used to correct the basis set superposition error. The potential has a planar T-shaped global minimum with a well depth of 177.48 cm-1 at the intermolecular distance of 3.72 Å. An additional planar local minimum is also found and is separated from the global minimum with an energy barrier with a height of 47.46 cm-1. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to calculate the rovibrational energy levels for three isotopic species of Ar-H2S complexes (Ar-H232S, Ar-H233S, and Ar-H234S). The rotational transition frequencies and structural parameters for the three isotopomers were also determined for the ground and the first excited states, which are all in good agreement with the available experimental values.

Lei, Jinping; Zhou, Yanzi; Xie, Daiqian

2012-02-01

134

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

Science.gov (United States)

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

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

2013-08-01

135

Co-amorphous simvastatin and glipizide combinations show improved physical stability without evidence of intermolecular interactions  

DEFF Research Database (Denmark)

The objective of this study was to prepare a co-amorphous drug/drug combination between two BCS class II drugs, simvastatin (SVS) and glipizide (GPZ). This pharmacologically relevant combination of two drugs could produce a promising candidate for formulations intended for combination therapy of metabolic disorders. The co-amorphous SVS-GPZ mixtures (molar ratios 2:1, 1:1 and 1:2) were prepared by mechanical activation (ball milling or cryomilling) and characterized with respect to their thermal properties, possible molecular interactions, dissolution properties and physical stability, and compared to the behaviour of pure amorphous forms and their physical mixtures. It was found that even though a molecular mixture was achieved with all SVS-GPZ mixture ratios, no molecular interactions between the drugs could be detected. By formation of co-amorphous single-phase mixtures, only the dissolution rate of GPZ could be improved. The co-amorphous mixtures showed improved stability compared to the pure amorphous forms and the amorphous physical mixtures. It was concluded that this was attributable to the molecular level mixing of SVS with GPZ upon milling, and GPZ is acting as an anti-plasticizer in these mixtures.

Löbmann, Korbinian; Strachan, Clare

2012-01-01

136

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

Science.gov (United States)

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

Albertí, M; Pirani, F; Laganà, A

2013-08-15

137

Intermolecular potential energy surface and thermophysical properties of the CH4-N2 system  

Science.gov (United States)

A five-dimensional potential energy surface (PES) for the interaction of a rigid methane molecule with a rigid nitrogen molecule was determined from quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the CCSD(T) level of theory was utilized to compute a total of 743 points on the PES. The interaction energies were calculated using basis sets of up to quadruple-zeta quality with bond functions and were extrapolated to the complete basis set limit. An analytical site-site potential function with nine sites for methane and five sites for nitrogen was fitted to the interaction energies. The PES was validated by calculating the cross second virial coefficient as well as the shear viscosity and binary diffusion coefficient in the dilute-gas limit for CH4-N2 mixtures. An improved PES was obtained by adjusting a single parameter of the analytical potential function in such a way that quantitative agreement with the most accurate experimental values of the cross second virial coefficient was achieved. The transport property values obtained with the adjusted PES are in good agreement with the best experimental data.

Hellmann, Robert; Bich, Eckard; Vogel, Eckhard; Vesovic, Velisa

2014-12-01

138

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

Directory of Open Access Journals (Sweden)

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

Xiu-Mei Mo

2011-03-01

139

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

Science.gov (United States)

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

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

2011-05-01

140

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

Science.gov (United States)

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

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

2013-07-01

 
 
 
 
141

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

Science.gov (United States)

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

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

2014-10-14

142

On the representation of the electric charge distribution in ethane for calculations of the molecular quadrupole moment and intermolecular electrostatic energy  

DEFF Research Database (Denmark)

It is shown that a simple atom-site monopole model is inferior to one which includes higher-order local multipoles to represent the intramolecular charge distribution of ethane. Unlike the latter model, the local monopole representation predicts the wrong sign for the molecular quadrupole moment 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 is copyrighted by The American Institute of Physics.

Hansen, Flemming Yssing; Alldredge, G. P.

1985-01-01

143

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

Science.gov (United States)

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

Suzuki, Furitsu; Nishiyama, Yusuke; Kaji, Hironori

2014-06-01

144

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2014-06-07

145

A Theoretical Study of Intermolecular Interaction and Hydrogen Bond for Furan with HCl and CH4-nCln (n = 0-3  

Directory of Open Access Journals (Sweden)

Full Text Available Furan has both the oxygen lone pair electrons and an aromatic ?-electron. The study of the interaction between furan as a proton acceptor and a proton donor is important to understand the properties of furan and the related hydrogen bond. The geometries, intermolecular energies and vibrational properties of the furan-HCl and furan-CH4-nCln (n = 0-3 complexes have been performed using the second order Moller-Plesset perturbation theory. The NBO analysis of the optimized geometries has also been performed. The optimized geometries of furan-HCl and furan-CH4-nCln (n = 0-3 show both the C(Cl-H...O and C(Cl-H...? interactions. In all of the optimized geometries of furan-CH4-nCln (n = 0-3, C-H bond lengths are shorten and vibrational frequencies are blue-shifted, while for the furan-HCl complex, C-H bond length is lengthened and vibrational frequencies are red-shifted. The NBO analysis shows that, for the furan-CH4-nCln (n = 0-3 complexes, the charge transfer from the lone pairs of the O atom to both ?*(CH antibonding MO and lone pairs of Cl atom, which is the important feature for blue-shifted hydrogen bond. Both lone pairs and ? electrons of furan can be acted as a proton acceptor interacting with a proton donor. Cl-H...O(? is a conventional hydrogen bond , while C-H...O(? is a blue-shifted hydrogen bond.

Daiqian Xie

2003-05-01

146

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

International Nuclear Information System (INIS)

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

147

Intramolecular photo-switching and intermolecular energy transfer as primary photoevents in photoreceptive processes: The case of Euglena gracilis  

International Nuclear Information System (INIS)

In this paper we report the results of measurements performed by FLIM on the photoreceptor of Euglenagracilis. This organelle consists of optically bistable proteins, characterized by two thermally stable isomeric forms: A498, non fluorescent and B462, fluorescent. Our data indicate that the primary photoevent of Euglena photoreception upon photon absorption consists of two contemporaneous different phenomena: an intramolecular photo-switch (i.e., A498 becomes B462), and a intermolecular and unidirectional Forster-type energy transfer. During the FRET process, the fluorescent B462 form acts as donor for the non-fluorescent A498 form of the protein nearby, which acts as acceptor. We hypothesize that in nature these phenomena follow each other with a domino progression along the orderly organized and closely packed proteins in the photoreceptor layer(s), modulating the isomeric composition of the photoreceptive protein pool. This mechanism guarantees that few photons are sufficient to produce a signal detectable by the cell.

148

New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular receptors. Here, we propose a new solvation free energy function through the improvement of the solvent-contact model, and test its applicability in estimating the solvation free energies of organic molecules with varying sizes and shapes. This new solvation free energy...

Choi Hwanho; Kang Hongsuk; Park Hwangseo

2013-01-01

149

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2013-08-29

150

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

Science.gov (United States)

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

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

2011-02-21

151

Intramolecular photo-switching and intermolecular energy transfer as primary photoevents in photoreceptive processes: The case of Euglena gracilis  

Energy Technology Data Exchange (ETDEWEB)

In this paper we report the results of measurements performed by FLIM on the photoreceptor of Euglenagracilis. This organelle consists of optically bistable proteins, characterized by two thermally stable isomeric forms: A{sub 498,} non fluorescent and B{sub 462}, fluorescent. Our data indicate that the primary photoevent of Euglena photoreception upon photon absorption consists of two contemporaneous different phenomena: an intramolecular photo-switch (i.e., A{sub 498} becomes B{sub 462}), and a intermolecular and unidirectional Forster-type energy transfer. During the FRET process, the fluorescent B{sub 462} form acts as donor for the non-fluorescent A{sub 498} form of the protein nearby, which acts as acceptor. We hypothesize that in nature these phenomena follow each other with a domino progression along the orderly organized and closely packed proteins in the photoreceptor layer(s), modulating the isomeric composition of the photoreceptive protein pool. This mechanism guarantees that few photons are sufficient to produce a signal detectable by the cell.

Mercatelli, Raffaella; Quercioli, Franco [Istituto Sistemi Complessi, CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Barsanti, Laura; Evangelista, Valter [Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa (Italy); Coltelli, Primo [ISTI, CNR, Via Moruzzi 1, 56124 Pisa (Italy); Passarelli, Vincenzo; Frassanito, Anna Maria [Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa (Italy); Gualtieri, Paolo, E-mail: paolo.gualtieri@pi.ibf.cnr.it [Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa (Italy)

2009-07-24

152

INTER-MOLECULAR INTERACTIONS OF TETRAHYDROPYRAN + 1-BUTANOL BINARY SYSTEM AT T= (298.15, 303.15, 308.15, 313.15 & 318.15 K  

Directory of Open Access Journals (Sweden)

Full Text Available The evaluation of the different thermo dynamical parameters such as isentropic compressibility, molar volume, free length, acoustic impedance, internal pressure with their excess E E values, excess velocity (u , deviations of isentropic compressibility (? K , excess molar volume (V , s m E E E excess free length (L , excess acoustic impedance (Z and excess internal pressure (ð over the entire f i range of composition have been carried out at T = (298.15, 303.15, 308.15, 313.15 & 318.15 K from the measurements of ultrasonic velocity (u and density (ñ of pure & binary liquid mixtures of tetrahydropyran (THP with 1-butanol. The results thus obtained are discussed for molecular interaction. The nature of these values as seen from the plots of these ultrasonic parameters with the composition range indicates presence of the intermolecular interaction between the components of molecules of the mixture.

Anil Kumar K

2014-06-01

153

Intermolecular energy transfer from UO22+ to Eu3+ in solutions  

International Nuclear Information System (INIS)

The quenching constants for the UO22+ ion fluorescence by the Eu3+ ion in H2O, D2O, potassium formate and acetic acid media were determined by measuring the decrease in intensity of the 5050 A fluorescence peak and the lifetime of the UO22+ ion fluorescence. The energy transferred to the Eu3+ ion was found to be a small fraction of the energy lost by the UO22+ ion by the non-radiative processes. The variations of the quenching constants of the UO22+ ion and the fluorescence lifetimes were determined for different concentrations of potassium formate and acetic acid. These results indicate that the UO22+ ion forms inner sphere complexes with the two ligands mentioned

154

Polyelectrolyte and non-polyelectrolyte polyacrylamide copolymer solutions: the role of salt on the intra- and intermolecular interactions  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in portuguese Poli(acrilamida-co-dihexilacrilamida) (PAHM-0) e poli(acrilamida-co-acrilato de sódio-co-dihexilacrilamida) (PAHM-21) foram estudadas por espalhamento de raios-X a baixos ângulos (SAXS), espalhamento de luz (LS) e reologia. Os resultados de SAXS ressaltaram o caráter polieletrolítico da PAHM-21, com [...] uma conformação altamente estendida em solução aquosa devido às repulsões entre as cargas, enquanto a PAHM-0 tem uma conformação em novelo aleatório. As medidas de LS indicaram que a PAHM-0 forma aglomerados intermoleculares em solução, na presença e na ausência de sal, mesmo com um conteúdo hidrofóbico menor que o descrito na literatura para poliacrilamidas associativas. Contudo, os resultados reológicos mostraram que, apesar de haver associação hidrofóbica, não há um aumento da viscosidade. Os resultados de LS da PAHM-21 sugerem que esse polímero forma, predominantemente, associações intramoleculares na presença de sais. Além disso, as medidas viscosimétricas mostram que a sua viscosidade diminui com a blindagem das cargas pela adição de sais. Abstract in english Poly(acrylamide-co-dihexylacrylamide) (PAHM-0) and poly(acrylamide-co-sodium acrylate-co-dihexylacrylamide) (PAHM-21) were studied through small-angle X-ray scattering (SAXS), light scattering (LS) and rheology. SAXS results highlighted the polyelectrolyte character of PAHM-21, with highly extended [...] conformation in aqueous solution owing to charge repulsion, while the PAHM-0 has a coil conformation. LS measurements indicated that PAHM-0 makes intermolecular clusters in solution, in presence and absence of salt, even with a lower hydrophobic content than that described in the literature to the associative polyacrylamides. However, the rheological results showed that there is not an enhancement of the viscosity although hydrophobic association takes place. LS results for PAHM-21 suggest that this polymer makes intramolecular associations mainly in the presence of salts. Furthermore, the viscosity measurements show that its viscosity decreases due to screening of the charges by the addition of salts.

Ana M. S., Maia; Marcos A., Villetti; Redouane, Borsali; Rosangela C., Balaban.

1871-18-01

155

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

Science.gov (United States)

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

Frezzato, Diego; Rastrelli, Federico; Bagno, Alessandro

2006-03-23

156

Electron dynamics and intermolecular energy transfer in aqueous solutions studied by X-ray electron spectroscopy  

Science.gov (United States)

X-ray photoelectron spectroscopy measurements from a vacuum liquid microjet are performed to investigate the electronic structure of aqueous solutions. Here, focus is on the excited-state dynamics of chloride and hydroxide anions in water, following core-level excitation. A series of Cl^-(aq) charge-transfer-to-solvent (CTTS) states, and their ultrafast relaxation, on the time scale of the core hole, is identified from the occurrence of spectator Auger decay. Resonant oxygen 1s excitation of aqueous hydroxide, in contrast, leads to non-local decay, involving energy transfer into a neighboring water molecule. This channel is argued to arise from the weak hydrogen donor bond of OH^-(aq), and thus identifies a special transient hydration configuration, which can explain hydroxide's unusual and fast transport in water. Analogous measurements from pure water point to a similar relaxation channel, which is concluded from a strong isotope effect. The characteristic resonance spectral features are considerably stronger for H2O(aq) than for D2O(aq). As for OH^-(aq) the results can be understood in terms of energy transfer from the excited water molecule to a neighbor water molecule.

Winter, Bernd

2009-03-01

157

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

Science.gov (United States)

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

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

2010-08-01

158

The study of intermolecular energy transfers in electronic energy quenching for molecular collisions N2-N2, N2-O2, O2-O2  

Directory of Open Access Journals (Sweden)

Full Text Available Contributions of intermolecular electron energy transfers in the electronic quenching are calculated for molecular collisions N2(A3?u+, W3?u+N2(X1?g+, v=0, N2(A3?u++N2(X1?g+, v?0, N2(A3?u++O2(X3?g?, v=0–2, O2(a1?g, b1?g++O2(X3?g?, v=0–2. The calculation has allowed one to estimate the product branching ratios. It is shown that there is a dependence of the calculated rate coefficients on the vibrational excitation of N2(X1?g+ and O2(X3?g? molecules. In many cases, the calculated rate coefficients have a good agreement with available experimental data.

A. S. Kirillov

2008-05-01

159

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

CERN Document Server

A Mn4 single-molecule magnet (SMM), with a well isolated spin ground state of S = 9/2, is used as a model system to study Landau-Zener (LZ) tunneling in the presence of weak intermolecular dipolar and exchange interactions. The anisotropy constants D and B are measured with minor hysteresis loops. A transverse field is used to tune the tunnel splitting over a large range. Using the LZ and inverse LZ method, it is shown that these interactions play an important role in the tunnel rates. Three regions are identified: (i) at small transverse fields, tunneling is dominated by single tunnel transitions; (ii) at intermediate transverse fields, the measured tunnel rates are governed by reshuffling of internal fields, (iii) at larger transverse fields, the magnetization reversal starts to be influenced by the direct relaxation process, and many-body tunnel events may occur. The hole digging method is used to study the next-nearest neighbor interactions. At small external fields, it is shown that magnetic ordering occ...

Wernsdorfer, W; Vinslava, A; Christou, G

2005-01-01

160

Intermolecular, ion-molecular and interionic interactions in solutions of lithium and tetrabutylammonium salts in mixtures of methanol with propylene carbonate  

International Nuclear Information System (INIS)

Interparticle interactions are investigated in solutions of LiI, LiBr, LiCl, LiNCS, (C4H9)4NI, (C4H9)4NBr, (C4H9)4NCl in mixtures of methanol with propylene carbonate in absence of self-association of molecules of methanol and in different salt concentrations by the methods of IR spectroscopy. Intermolecular and ion-molecular interactions are studied on IR absorption lines of valent vibrations of OH-groups of methanol (3300-3500 cm-1), interionic interaction - on lines of valent CN (2000-2100 cm-1) and deformation O-Cl-O (625 cm-1) vibrations of NVS- and ClO4- correspondingly. Concentrations of lithium complexes forming in solutions are calculated on intensities of valent absorption lines of OH-groups of methanol. In the case of salt concentration increase the content of complexes decreases. Ousting of solvent molecule by anions in complex happens so faster as electron-donor ability of it is higher

 
 
 
 
161

Intermolecular inter-ligand interaction in mixed ligand complexes of lanthanides(III) involving histidine and some amino acids  

International Nuclear Information System (INIS)

The formation constant studies on binary and mixed ligand complexes of Pr (III) and Nd (III) involving histidine (hist) as primary ligand and ?-alanine (?-ala), valine (val) or leucine (leu) as secondary ligands have been undertaken to evaluate the extra-stabilization in the mixed ligand complexes due to possible occurrence of intramolecular inter-ligand interaction. Stability quantifying parameters (? log k and ?? log k) indicate significant inter-ligand interaction. (author)

162

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

Science.gov (United States)

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

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

2010-04-01

163

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

Science.gov (United States)

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

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

2001-07-01

164

Study on the intermolecular interactions of alkylcobaloxime complexes (RCo(dmgH) 2L, dmgH=dimethylglyoxime, R=alkyl, L=H 2O or pyridine)  

Science.gov (United States)

A series of alkylcobaloxime complexes, [RCo(dmgH) 2L, where dmgH=dimethylglyoxime, R=alkyl, L=neutral monodentate axial ligand], i.e. (EtO 2C) 2C(Me)CH 2Co(dmgH) 2H 2O( 1), n-C 5H 11Co(dmgH) 2H 2O( 2), Br(CH 2) 4Co(dmgH) 2py( 3) and Br(CH 2) 4Co(dmgH) 2H 2O( 4), have been synthesized and characterized. Analysis and comparison of their crystal packing structures with that of our previous reported complexes, COOCH 3(CH 2) 2Co(dmgH) 2H 2O( 5) and c-C 6H 11Co(dmgH) 2H 2O( 6), disclose that one-dimensional ribbon-like zigzag hydrogen bonded networks in 1, 2 and 4 are sustained and controlled by self-assembly between dimethylglyoxime and coordinated water through O-H⋯O - interactions. And the further formation of different types of hydrogen bond linkages with the variation of the axial groups leads to creation of special 2D or 3D architectures. However, the crystal packing structure of 5 and 6 are absolutely different from 1, 2 and 4 due to conformational isomerism effect. Additionally, different types of the protons attachment at O-H⋯O - bridge are observed in 3 and 4, respectively, which is favorable to the intermolecular interactions.

Zhang, Xin; Song, Xin-Yi; Li, Yi-Zhi; Chen, Hui-Lan

2005-07-01

165

Refined ab initio intermolecular ground-state potential energy surface for the He-C2H2 van der Waals complex  

DEFF Research Database (Denmark)

A refined CCSD(T) intermolecular potential energy surface is developed for the He-C2H2 van der Waals complex. For this, 206 points on the intermolecular potential energy surface, evaluated using the CCSD(T) method and the aug-cc-pVQZ basis set extended with a set of 3s3p2d1f1g midbond functions, are fitted to a 15-parameter analytic function. The potential is characterised by minima of-24.21 cm-1 at distances between the rare gas atom and the C2H2 centre of mass of 4.3453 A?, and with the complex in a linear configuration. At intermediate distances the surface is rather similar to that developed previously by Munteanu and Ferna?ndez (J. Chem. Phys., 123, 014309, 2005) but differs notably at short range. The improved potential energy surface should, therefore, be particularly useful for computations of collision line broadening. Dynamical calculations of a number of rovibrational bound state energies and wave functions are presented. Inspection of the nodal surfaces of several low lying excited states shows that the complex is close to the free rotor limit.

Ferna?ndez, Berta; Henriksen, Christian

2013-01-01

166

Alkane sorption in molecular sieves: The contribution of ordering, intermolecular interactions and sorption on Brondsted acid sites  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Distinct molecular ordering of sorbed alkanes is observed in MFI zeolites when the chain length of the alkane is similar to the length of the zig-zag channels (i.e., with n-hexane and n-heptane). In contrast, sorbate-sorbate interactions lead to an increase of the heat of adsorption with increasing loading in large pore molecular sieves such as faujasites. The maximum heat released through these interactions is 80% of the heat of condensation of the substance adsorbed. At most three molecules...

Eder, Florian; Lercher, Johannes A.

1997-01-01

167

A quantum-chemical validation about the formation of hydrogen bonds and secondary interactions in intermolecular heterocyclic systems  

Directory of Open Access Journals (Sweden)

Full Text Available We have performed a detailed theoretical study in order to understand the charge density topology of the C2H4O···C2H2 and C2H4S···C2H2 heterocyclic hydrogen-bonded complexes. Through the calculations derived from Quantum Theory of Atoms in Molecules (QTAIM, it was observed the formation of hydrogen bonds and secondary interactions. Such analysis was performed through the determination of optimized geometries at B3LYP/6-31G(d,p level of theory, by which is that QTAIM topological operators were computed, such as the electronic density ?(r, Laplacian Ñ2?(r, and ellipticity ?. The examination of the hydrogen bonds has been performed through the measurement of ?(r, Ñ2?(r and ? between (O···H—C and (S···H—C, whereas the secondary interaction between axial hydrogen atoms H? and carbon of acetylene. In this insight, it was verified the existence of secondary interaction only in C2H4S···C2H2 complex because its structure is propitious to form multiple interactions.

Boaz Galdino Oliveira

2009-08-01

168

STUDY OF INTERMOLECULAR FORCES AND INTERACTIONS IN BINARY LIQUID MIXTURE CHLOROFORM, ACETONE, M-XYLENE, AND CYCLOHEXANE IN DMSO  

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Full Text Available Thermodynamic studies like density ( ? , ultrasonic speed ( u and excess molar volume ( Vm E of binary liquid mixture of Chloroform ,Acetone, m- Xylene ,Cyclohexane+ DMSO have been carried out over the different range of composition at 308.15 K. Thermodynamic parameters like isentropic compressibility Ks , interaction parameter, ?12 , Flory parameters, coefficients, Ai and standard deviations, ? (Y E have been computed from experimental findings.

Dheeraj Kumar

2014-05-01

169

Intra and inter-molecular interactions dictate the aggregation state of irinotecan co-encapsulated with floxuridine inside liposomes  

DEFF Research Database (Denmark)

PURPOSE: The inter/intramolecular interactions between drugs (floxuridine, irinotecan) and excipients (copper gluconate, triethanolamine) in the dual-drug liposomal formulation CPX-1 were elucidated in order to identify the physicochemical properties that allow coordinated release of irinotecan and floxuridine and maintenance of the two agents at a fixed, synergistic 1:1 molar ratio. METHODS: Release of irinotecan and floxuridine from the liposomes was assessed using an in vitro-release assay. Fluorescence, Nuclear Magnetic Resonance spectroscopy (NMR) and UV-Vis were used to characterize the aggregation state of the drugs within the liposomes. RESULTS: Coordinated release of the drugs from liposomes was disrupted by removing copper gluconate. Approximately 45% of the total irinotecan was detectable in the copper-containing CPX-1 formulation by NMR, which decreased to 19% without copper present in the liposomal interior. Formation of higher order, NMR-silent aggregates was associated with slower and uncoordinated irinotecan release relative to floxuridine and loss of the synergistic drug/drug ratio. Solution spectroscopy and calorimetry revealed that while all formulation components were required to achieve the highest solubility of irinotecan, direct drug-excipient binding interactions were absent. CONCLUSIONS: Long-range interactions between irinotecan, floxuridine and excipients modulate the aggregation state of irinotecan, allowing for simultaneous release of both drugs from the liposomes.

Dicko, Awa; Frazier, April A

2008-01-01

170

Local conformation and intermolecular interaction of rigid ring polymers are not always the same as the linear analogue: cyclic amylose tris(phenylcarbamate) in ? solvents.  

Science.gov (United States)

Small-angle X-ray scattering and static and dynamic light scattering measurements were made for cyclic amylose tris(phenylcarbamate) (cATPC) of which weight-average molar mass M(w) ranges from 1.3 × 10(4) to 1.5 × 10(5) to determine their z-average mean square radius of gyration z, particle scattering function P(q), hydrodynamic radius R(H), and second virial coefficient A2 in methyl acetate (MEA), ethyl acetate (EA), and 4-methyl-2-pentanone (MIBK). The obtained z, P(q), and R(H) data were analyzed in terms of the wormlike ring to estimate the helix pitch per residue h and the Kuhn segment length ?(-1) (the stiffness parameter, twice the persistence length). Both h and ?(-1) for cATPC in MEA, EA, and MIBK are smaller than those for linear amylose tris(phenylcarbamate) (ATPC) in the corresponding solvent and the discrepancy becomes more significant with increasing the molar volume of the solvent. This indicates that not every rigid ring has the same local helical structure and chain stiffness as that for the linear polymer in the M(w) range investigated while infinitely long ring chains should have the same local conformation. This conformational difference also affects A2. In actuality, negative A2 was observed for cATPC in MIBK at the ? temperature of linear ATPC whereas intermolecular topological interaction of ring polymers increases A2. PMID:23879791

Asano, Natsuki; Kitamura, Shinichi; Terao, Ken

2013-08-15

171

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

Science.gov (United States)

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

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

2015-02-01

172

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

Science.gov (United States)

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

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

2015-02-01

173

Hexacyanometalate Molecular Chemistry : Trinuclear CrNi2 Complexes; MicroSQUID Magnetisation Studies of Intermolecular Interactions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Three different CrNi2 complexes were synthesized. They differ from each other by the nature of the terminal ligand and of the counter anion : [Cr(CN)4[CN-Ni(tetren)]2]Cl, that crystallizes in two different crystallographic systems and [Cr(CN)4[CN-Ni(dienpy2)]2](ClO4). The ground state spin value is 7/2 for the three systems (ferromagnetic interaction between chromium(III) and nickel(II) ions). The magnetisation of the three CrNi2 complexes was measured using an array of micr...

Tiron, Raluca; Wernsdorfer, Wolfgang; Tuyeras, Fabien; Scuiller, Ariane; Marvaud, Valerie; Verdaguer, Michel

2003-01-01

174

Intermolecular interactions between HD-GYP and GGDEF domain proteins mediate virulence-related signal transduction in Xanthomonas campestris.  

Science.gov (United States)

In the plant pathogen Xanthomonas campestris pv. campestris (Xcc) a two component system comprising RpfG and the complex sensor kinase RpfC is implicated in sensing and responding to the cell-cell signaling molecule DSF to positively regulate the synthesis of virulence factors such as extracellular enzymes, biofilm structure and motility. RpfG is a two-component regulator with a CheY-like receiver domain attached to an HD-GYP cyclic di-GMP phosphodiesterase domain. In a recent paper we showed that that the physical interaction of RpfG with two proteins with a diguanylate cyclase (GGDEF) domain, acts to control a sub-set of RpfG-regulated virulence functions. These protein-protein interactions required the conserved GYP motif in the HD-GYP domain of RpfG and were dependent on DSF signaling. Here we discuss these findings, considering in particular different scenarios for the role of RpfG in multiple signaling pathways involving cyclic di-GMP that impinge on virulence. PMID:21178479

Ryan, Robert P; Dow, J Maxwell

2010-01-01

175

Competing intramolecular vs. intermolecular hydrogen bonds in solution.  

Science.gov (United States)

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

Nagy, Peter I

2014-01-01

176

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution  

Directory of Open Access Journals (Sweden)

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.

Peter I. Nagy

2014-10-01

177

Intermolecular and Surface Forces  

CERN Document Server

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

Israelachvili, Jacob N

2010-01-01

178

Intermolecular and surface forces  

CERN Document Server

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

Israelachvili, Jacob N

2011-01-01

179

Readout system for delay line detectors with a time stamp TDC and a small angle scattering study of intermolecular interactions in protein solutions  

Energy Technology Data Exchange (ETDEWEB)

The present work consists of two parts: The first part is a contribution to instrumentation and more particularly the development of a readout system for gas detectors used in small angle X-ray scattering (SAXS) and the second part covers the results of an investigation of interactions between proteins in solution. One aim of the instrumentation part was to investigate the role of fluorescence in gas proportional detector with delay line readout, a phenomenon that leads to events, unrelated to the actual scattering pattern. For this purpose a time stamp (TS-) TDC readout was developed that is able to detect simultaneous events in the detector by using all timing information in the anode and cathode signals (check-sum). It was found that the fluorescence of the gas clearly limits the spatial and time resolution in gas detection. The present observations confirm the influence of argon fluorescence on the point-spread function (PSF) and demonstrate that a rejection mechanism that analyses single events only cannot entirely eliminate these effects. The signal-to-noise ratio can, however, be improved by taking the drift time of the electrons and the check-sum of the signals into account. Drift time measurements are made possible by the unique ability of the TS-TDC to correlate the observation of scattered photons with individual radiation bunches in the storage ring. This feature could also facilitate time-resolved measurements with nanosecond-resolution. In the second part of this thesis gas detectors were used in a contribution to an important topic in biophysics: the study of intermolecular interactions in protein solutions. This was done by measuring the structure factors of protein solutions. According to the DLVO theory the main interactions between spherical particles are the hard-sphere interactions, a short range attraction, due to surface-surface forces, and a long range repulsion caused by the fact that the particles are charged. A computer program was written, which calculates the structure factors from the pair potentials and was shown to reproduce some results in the literature as well as all the main observations in our experiments. Several measurements were made on solutions of the proteins glucose oxidase and lysozyme under various conditions in order to investigate the interactions of these proteins in the presence of co-solutes such as salts, urea, TMAO, glycine or at different protein concentrations. The influence of variables like temperature and pH on the attractive and repulsive interactions and in particular the pair potentials was also studied. The main features of the structure factors observed in the protein concentration series are correctly predicted with the program. (orig.)

Niebuhr, M.

2004-07-01

180

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

Science.gov (United States)

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

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

1992-12-15

 
 
 
 
181

Studies on intermolecular interactions in (nitrobenzene + alkoxyethanol) binary mixtures by relative permittivity measurements at T = (293.15, 298.15, 303.15, 308.15, and 313.15) K  

International Nuclear Information System (INIS)

Highlights: ? Dielectric properties are presented. ? Results showed existence of hetero-molecular interactions. ? Stable intermolecular complexes are formed. - Abstract: Relative permittivities, at T = (293.15, 298.15, 303.15, 308.15, and 313.15) K, in the binary mixtures of nitrobenzene with 2-methoxyethanol, 2-ethoxyethanol, 2-propoxyethanol, and 2-butoxyethanol have been measured as a function of composition. From the experimental results, the deviations in the relative permittivity at T = (293.15, 298.15, 303.15, 308.15, and 313.15) K and the excesses of temperature coefficient of relative permittivity at T = 298.15 K from a mole fraction average have been calculated. The results are discussed in terms of intermolecular interactions and structure of studied binary mixtures.

182

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

International Nuclear Information System (INIS)

To further understanding of gas phase collision dynamics involving electronically-excited molecules, a fully quantum mechanical study of He + H2(B 1?/sub u/+) was undertaken. Iterative natural orbital configuration interaction (CI) calculations were performed to obtain the interaction potential between He and H2(B 1?/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 + H2(E,F 1?/sub g/+) and with He + H2(X 1?/sub g/+) and cause a local maximum and a deep minimum in the He + H2(B 1?/sub u/+) PES, respectively. The crossing with He + H2(X 1?/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 H2(B 1?/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

183

Intramolecular and intermolecular hydrogen bonds in aminophenols  

International Nuclear Information System (INIS)

IR-Fourier spectroscopy methods are adopted to study intramolecular and intermolecular hydrogen bonds that form in CCl4 solutions of aminophenol derivatives and in a solid phase of these compounds pressed in KBr. If a hydroxyl group is present in the molecule in the ortho-position to an amino group, then intramolecular interactions between OH and NH groups will take place in aminophenol solutions. Intramolecular O-HO=S=O and N-H...O=S=O hydrogen bonds are found in solutions of compounds containing a sulfonamide fragment. Additional acylation of the amino group causes an intramolecular O-H...O=C hydrogen bond to form in solutions. Functional groups OH, NH, SO2, and C=O interact with one another in various ways in the solid phase to form intermolecular hydrogen bonds in aminophenols. (authors) Keywords aminophenol - IR spectrum - intramolecular hydrogen bond - intermolecular hydrogen bond

184

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

Science.gov (United States)

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

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

2015-01-26

185

Low energy neutrino interactions  

International Nuclear Information System (INIS)

Rather than review low energy neutrino interactions, recently reported deuteron results are presented. Pion factory neutrino experiments are surveyed and reactor neutrino work is discussed. Finally the deuteron experiment itself is presented in terms of the approach, detector description, neutron detection efficiency, data, background tests, deuteron rates, and consistency checks. The results of a reactor experiment comparing the observed rates of the charged current and neutral current interactions of reactor neutrinos with deuterons gives an indication of neutrino instability at the 2 and 3 standard deviation level

186

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

Science.gov (United States)

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

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

2009-09-01

187

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

Science.gov (United States)

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

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

2013-02-01

188

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity  

Science.gov (United States)

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

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

2014-05-01

189

Symmetry in the polarization expansion for intermolecular forces  

International Nuclear Information System (INIS)

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

190

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

Science.gov (United States)

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

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

2014-10-21

191

Intermolecular C-H...N and C-H...O interactions in (2S,4S,5R)-(-)-3,4-dimethyl-5-phenyl-2-(1,3-thiazol-2-yl)-1,3-oxazolidine  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The title compound, C??H??N?OS, prepared from (1R,2S)-(-)-ephedrine, contains the oxazolidine ring in an envelope conformation, with the nitrogen atom 0.623 (2) Å from the plane of the other four oxazolidine ring atoms. Intermolecular C--H...N and C--H...O interactions generate a two-dimensional hydrogen-bonded network, with shortest C...N and C...O distances of 3.403 (3) and 3.463 (2) Å, respectively.

Fitzsimons, Lavelle M.; Gallagher, John F.

1999-01-01

192

Intermolecular N-H...O and C-H...O interactions form a two-dimensional network in (2S,4S,5R)-(-)-3,4-dimethyl-5-phenyl-2-(pyrrol-2-yl)-1,3-oxazolidine  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The title compound, C??H??N?0, prepared from (1R,2S)- (-)-ephedrine, crystallizes in space group P1 with two molecules in the asymmetric unit. The oxazolidine rings of the two molecules adopt an envelope conformation, with the N atom 0.609 (6) and 0.623 (6)Å from the plane of the other four oxazolidine ring atoms. Intermolecular Npyrrole--H...O and Cphenyl--H...O interactions generate a two-dimensional hydrogen-bonded network with N...O and C...O distances of 3.004 (...

Gallagher, John F.; Fitzsimons, Lavelle M.

1999-01-01

193

Intermolecular interactions in nuclear magnetic resonance: medium shifts of the 1H and 13C nuclei in methane in the gas phase and in solution and of gaseous 3He  

International Nuclear Information System (INIS)

An analysis has been carried out of the continuum and the binary collision models used in the description of NMR solvent shifts caused by Van der Waals intermolecular interactions. The basic assumption underlying the models, i.e. ? sub(w)= -BE2 (I) is examined. The possible effects on I of such phenomena as B anisotropy and field gradients are discussed, as well as the inadequacy of I in representing the true intermolecular shielding. A new expression for E2 is proposed, which in connection with I forms the bais of a modified binary collision model. The new E2 expression takes into account the dynamic character of the interaction. The major obstacle to the binary collision model, the requirement for accurate parameters for the intermolecular potential employed in the statistical-mechanical averaging, is alleviated by the establishment of priority rules to be used in the selection of these paramters. The proposed binary collision model and a collision model are used to interpret the 1H and 13C medium shifts of methane in the gas phase and in solution. The proton shift data conform equally well to either model; the 13C data indicate that a large solvent-dependent term contributes to the observed medium shifts in addition to I. Proton and 13C B parameters of methane in the gas phase and in solution are discussed. Preliminary results of 3He medium shifts as a function of gas density aium shifts as a function of gas density are presented. An extracted B parameter based on the proposed binary collision model appears to agree well with the result of a quantum-mechanical calculation of B for a 3He atom in a uniform static electric field. (LL)

194

Desensitization of metastable intermolecular composites  

Science.gov (United States)

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

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

2011-04-26

195

Intermolecular hydrogen bond energies in crystals evaluated using electron density properties: DFT computations with periodic boundary conditions.  

Science.gov (United States)

The hydrogen bond (H-bond) energies are evaluated for 18 molecular crystals with 28 moderate and strong O-H···O bonds using the approaches based on the electron density properties, which are derived from the B3LYP/6-311G** calculations with periodic boundary conditions. The approaches considered explore linear relationships between the local electronic kinetic G(b) and potential V(b) densities at the H···O bond critical point and the H-bond energy E(HB). Comparison of the computed E(HB) values with the experimental data and enthalpies evaluated using the empirical correlation of spectral and thermodynamic parameters (Iogansen, Spectrochim. Acta Part A 1999, 55, 1585) enables to estimate the accuracy and applicability limits of the approaches used. The V(b)-E(HB) approach overestimates the energy of moderate H-bonds (E(HB) < 60 kJ/mol) by ~20% and gives unreliably high energies for crystals with strong H-bonds. On the other hand, the G(b)-E(HB) approach affords reliable results for the crystals under consideration. The linear relationship between G(b) and E(HB) is basis set superposition error (BSSE) free and allows to estimate the H-bond energy without computing it by means of the supramolecular approach. Therefore, for the evaluation of H-bond energies in molecular crystals, the G(b) value can be recommended to be obtained from both density functional theory (DFT) computations with periodic boundary conditions and precise X-ray diffraction experiments. PMID:22786749

Vener, M V; Egorova, A N; Churakov, A V; Tsirelson, V G

2012-11-01

196

MRI Using Intermolecular Multiple-Quantum Coherences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Intermolecular multiple-quantum coherences (iMQCs) can generate NMR signals from exceedingly small dipolar interactions between distant spins in solutions. In the last few years, these signals have been used for a wide range of applications in imaging and high-resolution spectroscopy. Recent applications include MRI contrast enhancement, suppression of inhomogeneous broadening in NMR experiments, and more recently, in vivo temperature measurement. In this chapter, we describe how basic iMQC p...

Branca, Rosa Tamara

2011-01-01

197

Inhomogeneous and interacting vacuum energy  

CERN Document Server

Vacuum energy is a simple model for dark energy driving an accelerated expansion of the universe. If the vacuum energy is inhomogeneous in spacetime then it must be interacting. We present the general equations for a spacetime-dependent vacuum energy in cosmology, including inhomogeneous perturbations. We show how any dark energy cosmology can be described by an interacting vacuum+matter. Different models for the interaction can lead to different behaviour (e.g., sound speed for dark energy perturbations) and hence could be distinguished by cosmological observations. As an example we present the cosmic microwave microwave background anisotropies and the matter power spectrum for two different versions of a generalised Chaplygin gas cosmology.

De-Santiago, Josue; Wang, Yuting

2012-01-01

198

Inhomogeneous and Interacting Vacuum Energy  

Science.gov (United States)

Vacuum energy is a simple model for dark energy driving an accelerated expansion of the universe. If the vacuum energy is inhomogeneous in spacetime then it must be interacting. We present the general equations for a spacetime-dependent vacuum energy in cosmology, including inhomogeneous perturbations. We show how any dark energy cosmology can be described by an interacting vacuum+matter. Different models for the interaction can lead to different behaviour (e.g., sound speed for dark energy perturbations) and hence could be distinguished by cosmological observations. As an example we present the cosmic microwave microwave background anisotropies and the matter power spectrum for two different versions of a generalised Chaplygin gas cosmology.

De-Santiago, Josue; Wands, David; Wang, Yuting

199

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

Science.gov (United States)

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

Han, Li-Juan; Kong, Ya-Jie

2014-11-01

200

Quantum mechanical calculations on weakly interacting complexes  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Symmetry-adapted perturbation theory (SAPT) has been applied to compute the intermolecular potential energy surfaces and the interaction-induced electrical properties of weakly interacting complexes. Asymptotic (large R) expressions have been derived for the contributions to the collision-induced properties up to and including second order in the intermolecular potential. The computed interaction-induced polarizability for the helium diatom has been used in quantum-dynamical calculations of t...

Heijmen, Theodorus Gerardus Albertus

1998-01-01

 
 
 
 
201

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

Science.gov (United States)

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

Beck, John Frederick; Mo, Yirong

2007-01-15

202

Optimized intermolecular potential for nitriles based on Anisotropic United Atoms model  

Digital Repository Infrastructure Vision for European Research (DRIVER)

An extension of the Anisotropic United Atoms intermolecular potential model is proposed for nitriles. The electrostatic part of the intermolecular potential is calculated using atomic charges obtained by a simple Mulliken population analysis. The repulsion-dispersion interaction parameters for methyl and methylene groups are taken from transferable AUA4 literature parameters [Ungerer et al., J. Chem. Phys., 2000, 112, 5499]. Non-bonding Lennard-Jones intermolecular potential parameters are re...

Hadj-kali, Mohamed; Gerbaud, Vincent; Joulia, Xavier; Lacaze-dufaure, Corinne; Mijoule, Claude; Ungerer, Philippe

2008-01-01

203

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

Science.gov (United States)

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

Velaga, Srinath C; Anderson, Brian J

2014-01-16

204

Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy  

Science.gov (United States)

A scheme to calculate fully quantum mechanical (ab initio) interaction energy involving a macromolecule like protein is presented. In this scheme, the protein is decomposed into individual amino acid-based fragments that are treated with proper molecular caps. The interaction energy between any molecule and the given protein is given by the summation of interactions between the molecule and individually capped protein fragments. This scheme, termed molecular fractionation with conjugate caps (MFCC), makes it possible and practical to carry out full quantum mechanical (ab initio) calculation of intermolecular interaction energies involving proteins or other similar biological molecules. Numerical tests performed on the interaction energies between a water molecule and three small peptides demonstrate that the MFCC method can give excellent ab initio interaction energies compared to the exact treatment in which the whole peptides are included in the calculation. The current scheme scales linearly with the atomic size of the protein and can be directly applied to calculating real protein-molecule interaction energies by using fully quantum (ab initio) methods that are otherwise impossible. The success of the current method is expected to have a powerful impact in our prediction of protein interaction energies including, e.g., protein-drug interactions.

Zhang, Da W.; Zhang, J. Z. H.

2003-08-01

205

Expressing the electromagnetic interaction energy  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The interaction energy of a given distribution of electric charges and currents with an electromagnetic external field is expressed by the Cartesian components of the multipole tensors of this distribution. Special attention is paid to the reduction of these tensors to the symmetric traceless ones. Although one uses the Cartesian tensor components in the explicit calculations, the final results are given in consistent tensorial form.

Vrejoiu, C.

2003-01-01

206

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

Science.gov (United States)

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

Shimada, Rintaro; Hamaguchi, Hiro-o

2014-05-28

207

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

International Nuclear Information System (INIS)

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

208

Enthalpies of mixing and intermolecular interactions in N,N-dimethylformamide-chloroform systems at temperatures ranging between 288 and 308 K  

Science.gov (United States)

The thermal effects of N,N-dimethylformamide (DMF) and chloroform (ChF) dissolution in the ChF-DMF system are calorimetrically determined at 288, 298, and 308 K over the range of compositions. The partial molar enthalpies of the components are also calculated, along with the values for the enthalpies of mixing. It is found that mixing is a strongly exothermic process and depends only slightly on temperature. The enthalpy parameters of double and triple interactions between DMF molecules in ChF, and between ChF molecules in DMF, are determined using virial expansions.

Kustov, A. V.; Smirnova, N. L.; Berezin, M. B.

2014-02-01

209

Electroweak interactions at LEP energies  

International Nuclear Information System (INIS)

What determined the energies of LEP and the SLC? Essentially they were determined by the desire to produce the Z0 in e+e- collisions. Since the mass of the Z0 is of order 90 MeV we need electron and positron energies of at least 45 MeV in the collider. We can already produce Z0 at the SPS and Tevatron, so why was so much effort and money spent to produce them also at the new accelerators? The answer is that the e+e- collisions the Z0 particles are produced in the s channel, and are thus produced resonantly, and therefore copiously. We shall see that the resonance peak in e+e- ? f bar f is several hundred times the cross section off peak. In the terminology introduced by the nuclear physicists looking for funding of high intensity 1 GeV machines, LEP is a Z0 factory. Using LEP we can study the properties of the Z0, and of the electroweak interactions, with a detail and precision never before possible. It is already possible, after only short runs at LEP to see clearly the effects of the radiative corrections in the electroweak interactions. It has been the that the electroweak interaction is now entering a stage equivalent to the heady days of the Lamb shift in QED. In this paper, the author shows how to calculate some of the processes that have been, will be and may be observed at these energies in the production and decay of the Zn the production and decay of the Z0. This paper calculates the decay rate for Z0 ? f bar f, to exhibit the Z0 peak , and also calculate the forward-backward asymmetry in this process which permits an alternative measurement of the parameters of the interaction

210

[Effect of stress actions on some hematologic and biochemical parameters of rat blood and on energetic intermolecular interactions in lipid extract under effect of light radiation].  

Science.gov (United States)

Comparative study has been carried of effect of the three-day long starvation, running, and their combination on morphological parameters of rat blood, lipid metabolism, and activity of blood Na,K-ATPase. Different effect has been shown of these stress factors on the blood erythrocyte composition. Starvation is accompanied by the most pronounced release of stored erythrocyte into blood, which results in a significant decrease both of the total amount of reticulocytes and the complete absence of reticulocytes of the I stage of maturity (the youngest). The running on treadmill led to a significant increase of the total amount of blood reticulocytes and to multiple increase of immature reticulocytes (RC-I and RC-II), which can indicate some stress of the bone marrow erythroid stem line. The curve of acid resistance of blood reticulocytes has shown the animal to experience the greatest stress at a combination of starvation and running. Starvation and running produced different effects on blood lipid characteristics. The content of triacylglycerides (TAG) in blood rose by 40% at starvation and decreased by 30% at running, a similar tendency being found for index of atherogeneity. The fatty acid composition of blood phospholipids at running and its combination with starvation practically did not differ from control. A change of Na,K-ATPase, which is so characteristic of reaction to various kinds of stress, sharply fell at starvation (by 22%), but increased at running (by 13%) and decreased markedly at combination of these actions. Absorption spectra of lipid extracts of the whole blood of the rats submitted to various stress actions showed that extracted from blood (at different amount depending on the kind of action) is an organic substance with coupled bonds, which absorbs light in the diapason of 360-620 nm. The absorption of light in the diapason of 400-410 nm has been found to belong to the Soret band of ferroheme and ferriheme. The shift of the Soret band indicates electron transitions in the iron cation. By the change and disappearance of the Soret band, it is possible to judge about the processes occurring in the lipid extract. The disappearance of the Soret band in the lipid extract indicates formation in it of steady radicals as a result of the ferriheme disintegration due to accumulation of energy in porphyrin, which does not seem to occur in the blood cell membranes. The iron atom in the ferriheme molecule is known to accept electron and yields a part of energy probably to porphyrin. Then ferriheme yields electron and becomes ferriheme with excess of energy in porphyrin. Hence, at admission of the next electron to the iron atom the porphyrin molecule is to get rid of the energy obtained earlier to prevent its disintegration. The heme is possible to be an accumulator and distributor of energy in tissue. PMID:23401964

Zabelinski?, S A; Chebotareva, M A; Tavrovskaia, T V; Skverchinskaia, E A; Shukoliukova, E P; Maslov, M N; Krivchenko, A I

2012-01-01

211

Weak interactions at high energies  

International Nuclear Information System (INIS)

Review lectures are presented on the phenomenological implications of the modern spontaneously broken gauge theories of the weak and electromagnetic interactions, and some observations are made about which high energy experiments probe what aspects of gauge theories. Basic quantum chromodynamics phenomenology is covered including momentum dependent effective quark distributions, the transverse momentum cutoff, search for gluons as sources of hadron jets, the status and prospects for the spectroscopy of fundamental fermions and how fermions may be used to probe aspects of the weak and electromagnetic gauge theory, studies of intermediate vector bosons, and miscellaneous possibilities suggested by gauge theories from the Higgs bosons to speculations about proton decay. 187 references

212

Free energy decomposition analysis of bonding and nonbonding interactions in solution  

Science.gov (United States)

A free energy decomposition analysis algorithm for bonding and nonbonding interactions in various solvated environments, named energy decomposition analysis-polarizable continuum model (EDA-PCM), is implemented based on the localized molecular orbital-energy decomposition analysis (LMO-EDA) method, which is recently developed for interaction analysis in gas phase [P. F. Su and H. Li, J. Chem. Phys. 130, 074109 (2009)], 10.1063/1.3077917. For single determinant wave functions, the EDA-PCM method divides the interaction energy into electrostatic, exchange, repulsion, polarization, desolvation, and dispersion terms. In the EDA-PCM scheme, the homogeneous solvated environment can be treated by the integral equation formulation of PCM (IEFPCM) or conductor-like polarizable continuum model (CPCM) method, while the heterogeneous solvated environment is handled by the Het-CPCM method. The EDA-PCM is able to obtain physically meaningful interaction analysis in different dielectric environments along the whole potential energy surfaces. Test calculations by MP2 and DFT functionals with homogeneous and heterogeneous solvation, involving hydrogen bonding, vdW interaction, metal-ligand binding, cation-?, and ionic interaction, show the robustness and adaptability of the EDA-PCM method. The computational results stress the importance of solvation effects to the intermolecular interactions in solvated environments.

Su, Peifeng; Liu, Hui; Wu, Wei

2012-07-01

213

High-Energy Neutrino Interactions  

CERN Multimedia

This experiment studies neutrino interactions in iron at the highest available energies using the narrow-band neutrino beam N3 and the wide-band neutrino beam N1. The basis of the detector is a massive target-calorimeter in which the energy deposited by a neutrino (or antineutrino) is measured by electronic techniques and the momentum of outgoing muons is determined by magnetic deflection. The detector is constructed in the form of a 20 m long iron-cored toroidal magnet, composed of modules of length 70~cm and 90~cm, and of 3.75~m diameter. Drift chambers placed in between each module measure the trajectory of muons from the neutrino interactions. The modules are of three types. The first ten modules are constructed of 2.5~cm iron plates with 20~scintillator planes inserted between the plates. The next five modules are constructed of 5~cm plates with 15~planes of scintillator and the last six modules are constructed of 15~cm plates with 5~planes of scintillators. The total mass of the detector is @=~1400 tons...

2002-01-01

214

On the importance of multi-body intermolecular energies in cluster formation, solvents effects, bulk properties of condensed matter and surface adsorption  

International Nuclear Information System (INIS)

We shall here present a review of the present knowledge concerning the role played by multi-body terms (fundamentally up to three, four and five-body terms) in the behaviour of dense states of matter such as oligomer bound states, crystalline structures, adsorption properties of surfaces and solvent effects. It is shown that relatively little effort has been carried out in these directions, mostly based on quantum mechanical studies of the intermolecular potentials of small closed-shell atomic clusters. The latter studies have been systematically developed for a series of elements, with relatively accurate molecular orbital calculations and apparently it would be quite fruitful to attempt more extensive applications thereof. Furthermore, where these applications have been attempted, it has been shown that: a) Non-additive effects may have a crucial, perhaps decisive role in the behaviour of the physical systems considered and b) the analysis of the multi-body terms can give insight as to how to address a calculation on a many-atom system saving the expense implied in the usual ''trial and error'' approach. (author)

215

Self-interacting Dark Matter Energy Density  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We investigate cosmological implications of an energy density contribution arising by elastic dark matter self-interactions. Its scaling behaviour shows that it can be the dominant energy contribution in the early universe. Constraints from primordial nucleosynthesis give an upper limit on the self-interaction strength which allows for the same strength as standard model strong interactions. Furthermore we explore the cosmological consequences of an early self-interaction do...

Stiele, Rainer; Boeckel, Tillmann; Schaffner-bielich, Jurgen

2011-01-01

216

Desensitization and recovery of metastable intermolecular composites  

Science.gov (United States)

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

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

2010-09-07

217

Potential energy surface for the benzene dimer and perturbational analysis of pi-pi interactions.  

Science.gov (United States)

We present a complete 6-dimensional potential energy surface for the benzene dimer obtained using symmetry-adapted perturbation theory (SAPT) of intermolecular interactions based on Kohn-Sham's description of monomers. Ab initio calculations were performed for 491 dimer geometries in a triple-zeta-quality basis set supplemented by bond functions. An accurate analytic fit to the ab initio results has been developed and low-energy stationary points on the potential energy surface have been found. We have determined that there are three minima on the surface. Two of them, the tilted T-shape and the parallel-displaced, are nearly isoenergetic with interaction energies of -2.77 and -2.74 kcal/mol, respectively. The third minimum, a twisted edge-to-edge conformation, is significantly less attractive, with the interaction energy equal to -1.82 kcal/mol. Both the T-shape and sandwich geometries, sometimes assumed to be minima, are shown to be only saddle points. The potential energy surface is extremely flat between the two lowest minima, the barrier being only 0.10 kcal/mol above the global minimum. The second-virial coefficient obtained with the new potential agrees well with experimental results over a wide range of temperatures. The SAPT approach rigorously decomposes the interaction energy into physical components. The relative importance of these components has been analyzed. PMID:16928128

Podeszwa, Rafa?; Bukowski, Robert; Szalewicz, Krzysztof

2006-08-31

218

Inconsistences in Interacting Agegraphic Dark Energy Models  

Digital Repository Infrastructure Vision for European Research (DRIVER)

It is found that the origin agegraphic dark energy tracks the matter in the matter-dominated epoch and then the subsequent dark-energy-dominated epoch becomes impossible. It is argued that the difficulty can be removed when the interaction between the agegraphic dark energy and dark matter is considered. In the note, by discussing three different interacting models, we find that the difficulty still stands even in the interacting models. Furthermore, we find that in the inte...

Sun, C. Y.; Song, Yu

2010-01-01

219

Simple non-empirical procedure for spin-component-scaled MP2 methods applied to the calculation of dissociation energy curve of noncovalently-interacting systems  

CERN Document Server

We present a simple and non-empirical method to determine optimal scaling coefficients, within the (spin-component)-scaled MP2 approach, for calculating intermolecular potential energies of noncovalently-interacting systems. The method is based on an observed proportionality between (spin-component) MP2 and CCSD(T) energies for a wide range of intermolecular distances and allows to compute with high accuracy a large portion of the dissociation curve at the cost of a single CCSD(T) calculation. The accuracy of the present procedure is assessed for a series of noncovalently-interacting test systems: the obtained results reproduce CCSD(T) quality in all cases and definitely outperform conventional MP2, CCSD and SCS-MP2 results. The difficult case of the Beryllium dimer is also considered.

Grabowski, I; Della Sala, F

2013-01-01

220

Inelastic scattering calculations in polyatomic systems using an ab initio intermolecular potential energy surface: The CO2* (0,0,1,0)+H2(D2) ?CO2(0,0,0,0)+H2(D2) systems  

International Nuclear Information System (INIS)

An ab initio computation of the energy transfer dynamics in the (CO2,H2) and (CO2,D2) systems has been carried out. The intermolecular potential energy hypersurface has been obtained from the results of ab initio SCF computations using extended Gaussian basis sets. The potential energy has been computed for 1053 different geometries. Previously formulated cubic spline fitting procedures are employed to effect surface interpolation and to extract surface gradients. At small CO2--H2 center-of-mass separations, the potential energy is repulsive and nearly exponential in form. At larger separations, small attractive wells are found. At a given separation, the most stable conformation is a planar, parallel structure of C2/sub v/ symmetry. Vibrational deexcitation probabilities, energy transfer mechanisms, and isotope ratios for the relaxation of the first excited state of the doubly degenerate bending mode of CO2 have been computed as a function of temperature by quasiclassical trajectories. In the temperature range below 600 K, the computed deexcitation probabilities are in fair to good agreement with the experimental shock tube data. At higher temperatures up to 1500 K, the computed results are too large by a factor of 3 or less. This error is interpreted to result at least partly from the assumption of classical motion. Computed isotope ratios are in fair accord with experiment over s are in fair accord with experiment over a 1000 K temperature range. The major relaxation mechanism is found to be V?R energy transfer for T< or =700 K and V?T transfer for 700 K< T< or =1500 K

 
 
 
 
221

Characterization of the dispersion interactions and an ab initio study of van der Waals potential energy parameters for coinage metal clusters.  

Science.gov (United States)

Dispersion interactions and van der Waals C(6) coefficients are studied in small model systems involving copper, silver, and gold atoms. We investigate a novel method where the intermolecular dispersion interactions are characterized by interatomic C(6) coefficients that can be used to formulate the dispersion energy as a separate contribution to the total interaction energy at long distances. We obtain the C(6) coefficients from a least-squares fit to the interaction energy surface. Other significant effects to the long-range interaction energy such as multipole-multipole and induction energy are explicitly taken into account. The electronic structure calculations are performed at the coupled cluster level including single, double, and perturbative triple excitations (CCSD(T) level) with triple-? basis sets. PMID:23102100

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

2012-11-29

222

Configuration Interactions Constrained by Energy Density Functionals  

CERN Document Server

A new method for constructing a Hamiltonian for configuration interaction calculations with constraints to energies of spherical configurations obtained with energy-density-functional (EDF) methods is presented. This results in a unified model that reproduced the EDF binding-energy in the limit of single-Slater determinants, but can also be used for obtaining energy spectra and correlation energies with renormalized nucleon-nucleon interactions. The three-body and/or density-dependent terms that are necessary for good nuclear saturation properties are contained in the EDF. Applications to binding energies and spectra of nuclei in the region above 208Pb are given.

Brown, B Alex; Hjorth-Jensen, Morten

2010-01-01

223

The inclusion of electron correlation in intermolecular potentials: Applications to the formamide dimer and liquid formamide  

DEFF Research Database (Denmark)

A test of the quality of the electrostatic properties and polarizabilities used in the nonempirical molecular orbital (NEMO) potential is carried out for formamide by calculating the molecular dipole moment and polarizability at the second-order Moller-Plesset (MP2) level of theory. The molecular dipole moment is 11% lower at the MP2 level than at the Hartree-Fock (HF) level, whereas the isotropic part of the polarizability is increased by 36% by adding electron correlation and using a considerably larger basis set. The atomic charges, dipole moments and polarizabilities obtained at the HF level are rescaled to get the correct molecular properties at the MP2 level. The potential minimum for the cyclic dimer of formamide is -17.50 kcal/mol with the MP2-scaled properties and is significantly lower than other potentials give. Two intermolecular potentials are constructed and used in subsequent molecular dynamics simulations: one with the regular NEMO potential and the other with the rescaled MP2 properties. A damping of the electrostatic field at short intermolecular distances is included in the present NEMO model. The average energies for liquid formamide are lower for the MP2-scaled model and are in good agreement with experimental results. The lowering of the simulation energy for the MP2-scaled potential indicates the strong dispersive interactions in liquid formamide.

Brdarski, S.; Åstrand, P.-O.

2000-01-01

224

RCUK-DST Smart Energy Grids and Energy Storage Interaction ...  

Eligibility for Research Council funding · How to apply for research funding ... \\Information on careers and other researcher development studies · Policy & ... \\RCUK-DST Smart Energy Grids and Energy Storage Interaction Meeting ... of \\research opportunity and expertise in the area of Smart Energy Grids and Energy \\Storage.

225

Pion nucleon interaction at low energy  

International Nuclear Information System (INIS)

A theory of the ?N interaction at low energy is described. An analogy is made with an unusual approach to potential scattering theory. Phase shifts, cross sections, and scattering amplitudes and lengths are calculated. 28 references

226

Ion-surface interactions at low energies  

International Nuclear Information System (INIS)

Ion-surface interactions in the low energy range (around 1 keV) can be understood to some extent using simple models such as single two-body collision processes or undisturbed electronic energy levels. More detailed investigations show that multiple collisions, shadowing and different neutralization processes for bulk and surface scattering have to be considered. For a complete description of the interaction a three dimensional treatment is necessary, including trajectory dependent neutralization. (Author)

227

Vacuum energies and multipole interactions  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english In this paper, we present a quantum-field-theoretical description of the interaction between stationary and localized external sources linearly coupled to bosonic fields (specifically, we study models with a scalar and the Maxwell field). We consider external sources that simulate not only point cha [...] rges but also higher-multipole distributions along D-dimensional branes. Our results complement the ones previously obtained in reference [1].

F.A., Barone; G., Flores-Hidalgo.

2010-06-01

228

Correlated ab initio investigations on the intermolecular and intramolecular potential energy surfaces in the ground electronic state of the O2-(X2?g)-HF(X1?+) complex  

Science.gov (United States)

This work reports the first highly correlated ab initio study of the intermolecular and intramolecular potential energy surfaces in the ground electronic state of the O_2^ - (X{}^2? _g) - HF(X{}^1?^+) complex. Accurate electronic structure calculations were performed using the coupled cluster method including single and double excitations with addition of the perturbative triples correction [CCSD(T)] with the Dunning's correlation consistent basis sets aug-cc-pVnZ, n = 2-5. Also, the explicitly correlated CCSD(T)-F12a level of theory was employed with the AVnZ basis as well as the Peterson and co-workers VnZ-F12 basis sets with n = 2 and 3. Results of all levels of calculations predicted two equivalent minimum energy structures of planar geometry and Cs symmetry along the A? surface of the complex, whereas the A' surface is repulsive. Values of the geometrical parameters and the counterpoise corrected dissociation energies (Cp-De) that were calculated using the CCSD(T)-F12a/VnZ-F12 level of theory are in excellent agreement with those obtained from the CCSD(T)/aug-cc-pV5Z calculations. The minimum energy structure is characterized by a very short hydrogen bond of length of 1.328 Å, with elongation of the HF bond distance in the complex by 0.133 Å, and De value of 32.313 Kcal/mol. Mulliken atomic charges showed that 65% of the negative charge is localized on the hydrogen bonded end of the superoxide radical and the HF unit becomes considerably polarized in the complex. These results suggest that the hydrogen bond is an incipient ionic bond. Exploration of the potential energy surface confirmed the identified minimum and provided support for vibrationally induced intramolecular proton transfer within the complex. The T-shaped geometry that possesses C2v symmetry presents a saddle point on the top of the barrier to the in-plane bending of the hydrogen above and below the axis that connects centers of masses of the monomers. The height of this barrier is 7.257 Kcal/mol, which is higher in energy than the hydrogen bending frequency by 909.2 cm-1. The calculated harmonic oscillator vibrational frequencies showed that the H-F stretch vibrational transition in the complex is redshifted by 2564 cm-1 and gained significant intensity (by at least a factor of 30) with respect to the transition in the HF monomer. These results make the O_2^ - - HF complex an excellent prototype for infrared spectroscopic investigations on open-shell complexes with vibrationally induced proton transfer.

Fawzy, Wafaa M.; Elsayed, Mahmoud; Zhang, Yuchen

2013-01-01

229

Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction.  

Science.gov (United States)

Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. PMID:19603501

Wang, Ling; Stumm, Boris; Helms, Volkhard

2010-03-01

230

Multiplicities in high energy interactions  

International Nuclear Information System (INIS)

Charged particle multiplicities in hadronic collision have been measured for all energies up to ?s = 540 GeV in the center of mass. Similar measurements in e+e- annihilation cover the much smaller range - up to ?s = 40 GeV. Data are also available from deep inelastic neutrino scattering up to ?s approx. 10 GeV. The experiments measure the mean charged multiplicity , the rapidity density at y = O, and the distributions in prong number. The mean number of photons associated with the events can be used to measure the ?0 and eta0 multiplicities. Some information is also available on the charged pion, kaon, and nucleon fractions as well as the K0 and ?0 rates and for the higher energy data, the identically equal fraction. We review this data and consider the implications of extrapolations to SSC energies. 13 references

231

Generalized Interacting Holographic Dark Energy Model  

CERN Document Server

In this manuscript, we present a generalization of the interacting holographic dark energy model using two equations of states for the dark energy: the modified variable Chaplygin gas and the viscous generalized Chaplygin gas. The dynamics of the model are expressed by the use of scalar fields and the scalar potentials.

Rashid, Muneer Ahmad; Jamil, Mubasher

2009-01-01

232

Dark energy interacting with two fluids  

CERN Document Server

A cosmological model of dark energy interacting with dark matter and another general component of the universe is investigated. We found general constraints on these models imposing an accelerated expansion. The same is also studied in the case for holographic dark energy.

Cruz, Norman; Pena, Francisco

2008-01-01

233

Dark energy interacting with two fluids  

Energy Technology Data Exchange (ETDEWEB)

A cosmological model of dark energy interacting with dark matter and another general component of the universe is investigated. We found general constraints on these models imposing an accelerated expansion. The same is also studied in the case for holographic dark energy.

Cruz, Norman [Departamento de Fisica, Facultad de Ciencia, Universidad de Santiago, Casilla 307, Santiago (Chile)], E-mail: ncruz@lauca.usach.cl; Lepe, Samuel [Instituto de Fisica, Facultad de Ciencias Basicas y Matematicas, Universidad Catolica de Valparaiso, Avenida Brasil 2950, Valparaiso (Chile)], E-mail: slepe@ucv.cl; Pena, Francisco [Departamento de Ciencias Fisicas, Facultad de Ingenieria, Ciencias y Administracion, Universidad de La Frontera, Avda. Francisco Salazar 01145, Casilla 54-D Temuco (Chile)], E-mail: fcampos@ufro.cl

2008-05-29

234

Determination of intermolecular transfer integrals from DFT calculations  

Energy Technology Data Exchange (ETDEWEB)

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.

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

2010-07-01

235

Casimir energy of frequency dependent interactions  

Science.gov (United States)

Vacuum polarization (or Casimir) energies can be straightforwardly computed from scattering data for static field configurations whose interactions with the fluctuating field are frequency independent. In effective theories, however, such interactions are typically frequency dependent. As a consequence, the relationship between scattering data and the Green's function is modified, which may or may not induce additional contributions to the vacuum polarization energy. We discuss several examples that naturally include frequency dependent interactions: (i) scalar electrodynamics with a static background potential, (ii) an effective theory that emerges from integrating out a heavy degree of freedom, and (iii) quantum electrodynamics coupled to a frequency dependent dielectric material. In the latter case, we argue that introducing dissipation as required by the Kramers-Kronig relations requires the consideration of the Casimir energy within a statistical mechanics formalism, while in the absence of dissipation, we can work entirely within field theory, using an alternative formulation of the energy density.

Graham, N.; Quandt, M.; Weigel, H.

2014-10-01

236

Problems with Ultrahigh-energy Neutrino Interactions  

CERN Document Server

The IceCube collaboration has recently identified events due to ultrahigh-energy neutrino interactions. Predictions of the neutrino-nucleon cross section at ultrahigh energies require a huge extrapolation of the cross sections experimentally measured at laboratory energies. Upon relating neutrino scattering to deep inelastic electron scattering, we show that the empirically verified color dipole picture is well suited for such an extrapolation. The dominant contribution to the total neutrino-nucleon cross section, even at ultrahigh energies, is due to the kinematic range where color transparency is valid for the color dipole interaction. We deviate from various claims in the literature on the presence of screening effects due to non-linear evolution at ultrahigh neutrino energies.

Schildknecht, Dieter

2014-01-01

237

Reactions of (MeC[sub 5]H[sub 4])[sub 3]/U(t-Bu): Intermolecular fluorine atom abstraction from fluorocarbons including saturated perfluorocarbons  

Energy Technology Data Exchange (ETDEWEB)

Only a few examples of intermolecular C-F bond activation have been reported. The pronounced inertness of perfluorocarbons is undoubtedly caused by the high C-F bond dissociation energies and by the weakness of metal-fluorocarbon interactions. We report the reactions of (MeC[sub 5]H[sub 4])[sub 3]/-U(t-Bu) with fluorocarbons, resulting in efficient fluorine abstraction under mild conditions in the presence of hydrocarbon solvents. To our knowledge, this is the first example of intermolecular C-F activation of a saturated fluorocarbon by a neutral d- or f-transition-metal complex and is not limited to tertiary C-F bonds. 18 refs.

Weydert, M.; Andersen, R.A.; Bergman, R.G. (Univ. of California, Berkeley, CA (United States) Lawrence Berkeley Lab., CA (United States))

1993-09-22

238

Interacting holographic dark energy with entropy corrections  

CERN Document Server

The holographic dark energy (HDE) is considered to be the most promising candidate of dark energy. Its definition is originally motivated from the entropy-area relation which depends on the theory of gravity under consideration. Recently a new definition of HDE is proposed with the help of quantum corrections to the entropy-area relation in the setup of loop quantum cosmology. Using this new definition, we investigate the model of interacting dark energy and derive its effective equation of state. Finally we establish a correspondence between generalized Chaplygin gas and entropy-corrected holographic dark energy.

Jamil, Mubasher

2010-01-01

239

Interacting holographic dark energy with logarithmic correction  

International Nuclear Information System (INIS)

The holographic dark energy (HDE) is considered to be the most promising candidate of dark energy. Its definition is motivated from the entropy-area relation which depends on the theory of gravity under consideration. Recently a new definition of HDE is proposed with the help of quantum corrections to the entropy-area relation in the setup of loop quantum cosmology. Employing this new definition, we investigate the model of interacting dark energy and derive its effective equation of state. Finally we establish a correspondence between generalized Chaplygin gas and entropy-corrected holographic dark energy

240

Interacting holographic dark energy with logarithmic correction  

Energy Technology Data Exchange (ETDEWEB)

The holographic dark energy (HDE) is considered to be the most promising candidate of dark energy. Its definition is motivated from the entropy-area relation which depends on the theory of gravity under consideration. Recently a new definition of HDE is proposed with the help of quantum corrections to the entropy-area relation in the setup of loop quantum cosmology. Employing this new definition, we investigate the model of interacting dark energy and derive its effective equation of state. Finally we establish a correspondence between generalized Chaplygin gas and entropy-corrected holographic dark energy.

Jamil, Mubasher; Farooq, M. Umar, E-mail: mjamil@camp.nust.edu.pk, E-mail: mufarooq@yahoo.com [Center for Advanced Mathematics and Physics, National University of Sciences and Technology, Rawalpindi, 46000 (Pakistan)

2010-03-01

 
 
 
 
241

Asymmetric intermolecular Heck reaction of aryl halides.  

Science.gov (United States)

The asymmetric intermolecular Heck reaction has been limited to aryl and vinyl triflates. Herein, we extend the reaction to aryl and vinyl bromides. Various cyclic olefins coupled with high enantioselectivity. Only bisphosphine oxides on a spiro backbone formed highly stereoselective Pd catalysts. The use of alcoholic solvents and alkylammonium salts were essential to promote halide dissociation from neutral arylpalladium complexes. PMID:24383764

Wu, Chunlin; Zhou, Jianrong Steve

2014-01-15

242

An improved intermolecular potential for sulfur hexafluoride  

International Nuclear Information System (INIS)

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

243

Weak interactions are weak at high energies  

Science.gov (United States)

We use a Schrödinger picture version of the instanton calculus to analyze the suggestion that nonperturbative instanton effects, such as baryon number violation in the electroweak interaction, can become large in high-energy scattering. We confirm that the euclidean instanton results of Ringwald, Espinosa and others are correct, for models with instantons of definite size, at low energy, and present a physical explanation of the energy dependence of amplitudes found by these authors. However, we show that their dilute instanton gas approximation breaks down at higher energy. Our techniques permit us to extend the energy regine in which a reliable calculation can be done. We find that the basic e 1/? suppression of the total cross section for instanton-induced processes persists at all energies, even ˜ M/?.

Banks, Tom; Farrar, Glennys; Dine, Michael; Karabali, Dimitra; Sakita, Bunji

1990-12-01

244

Binding energies of hypernuclei and ?-nuclear interactions  

International Nuclear Information System (INIS)

Variational calculations indicate that a reasonable description of ?p scattering and of ? separation energies can be obtained in terms of ?N plus dispersive and TPE ?NN forces. Results for the ?? interaction and for 6/sub ?/He obtained from an analysis of 10/sub ??/Be are discussed. Coulomb and ?N charge symmetry breaking effects in the A = 4 hypernuclei are discussed

245

Low-energy Antiproton Interaction with Helium  

Digital Repository Infrastructure Vision for European Research (DRIVER)

An ab initio potential for the interaction of the neutral helium atom with antiprotons and protons is calculated using the Born-Oppenheimer approximation. Using this potential, the annihilation cross section for antiprotons in the energy range 0.01 microvolt to 1 eV is calculated.

Gibbs, W. R.

1997-01-01

246

Characterization of low density lipoprotein receptor ligand interactions by fluorescence resonance energy transfer.  

Science.gov (United States)

The low density lipoprotein receptor (LDLR) is the prototype of a family of cell surface receptors involved in a wide range of biological processes. A soluble low density lipoprotein receptor (sLDLR) and a tryptophan (Trp)-deficient variant human apolipoprotein E3 (apoE3) N-terminal domain (NT) were used in binding studies. The sole cysteine in apoE3-NT was covalently modified with an extrinsic fluorescence probe, N-(iodoacetyl)-N'-(5-sulfo-1-napthyl)ethylenediamine (AEDANS), and the protein was complexed with lipid. Incubation of sLDLR with AEDANS-Trp-null apoE3-NT dimyristoylphosphatidylcholine (DMPC) disks, but not lipid-free AEDANS-apoE, induced an enhancement in AEDANS fluorescence emission intensity (excitation, 280 nm) consistent with intermolecular energy transfer from excited Trp in sLDLR to receptor-bound apoE. Ligand binding to sLDLR required calcium and was saturable. In competition binding assays, unlabeled apoE3-NT DMPC inhibited AEDANS-apoE DMPC binding to sLDLR more effectively than low density lipoprotein. Fluorescence changes in this system reflected pH-dependent ligand binding and release from sLDLR consistent with models derived from the X-ray crystal structure of the receptor at endosomal pH. Intermolecular energy transfer from excited Trp in LDLR family members to fluorescently tagged ligands represents a sensitive and convenient assay for the characterization of the myriad molecular interactions ascribed to this family of receptor. PMID:16467279

Yamamoto, Taichi; Lamoureux, Johanne; Ryan, Robert O

2006-05-01

247

Correlated ab initio investigations on the intermolecular and intramolecular potential energy surfaces in the ground electronic state of the O2(-)(X2?g)-HF(X1?+) complex.  

Science.gov (United States)

This work reports the first highly correlated ab initio study of the intermolecular and intramolecular potential energy surfaces in the ground electronic state of the O(2)(-)(X(2)?(g))-HF(X(1)?(+)) complex. Accurate electronic structure calculations were performed using the coupled cluster method including single and double excitations with addition of the perturbative triples correction [CCSD(T)] with the Dunning's correlation consistent basis sets aug-cc-pVnZ, n = 2-5. Also, the explicitly correlated CCSD(T)-F12a level of theory was employed with the AVnZ basis as well as the Peterson and co-workers VnZ-F12 basis sets with n = 2 and 3. Results of all levels of calculations predicted two equivalent minimum energy structures of planar geometry and C(s) symmetry along the A" surface of the complex, whereas the A' surface is repulsive. Values of the geometrical parameters and the counterpoise corrected dissociation energies (Cp-D(e)) that were calculated using the CCSD(T)-F12a/VnZ-F12 level of theory are in excellent agreement with those obtained from the CCSD(T)/aug-cc-pV5Z calculations. The minimum energy structure is characterized by a very short hydrogen bond of length of 1.328 Å, with elongation of the HF bond distance in the complex by 0.133 Å, and D(e) value of 32.313 Kcal/mol. Mulliken atomic charges showed that 65% of the negative charge is localized on the hydrogen bonded end of the superoxide radical and the HF unit becomes considerably polarized in the complex. These results suggest that the hydrogen bond is an incipient ionic bond. Exploration of the potential energy surface confirmed the identified minimum and provided support for vibrationally induced intramolecular proton transfer within the complex. The T-shaped geometry that possesses C(2v) symmetry presents a saddle point on the top of the barrier to the in-plane bending of the hydrogen above and below the axis that connects centers of masses of the monomers. The height of this barrier is 7.257 Kcal/mol, which is higher in energy than the hydrogen bending frequency by 909.2 cm(-1). The calculated harmonic oscillator vibrational frequencies showed that the H-F stretch vibrational transition in the complex is redshifted by 2564 cm(-1) and gained significant intensity (by at least a factor of 30) with respect to the transition in the HF monomer. These results make the O(2)(-)-HF complex an excellent prototype for infrared spectroscopic investigations on open-shell complexes with vibrationally induced proton transfer. PMID:23298038

Fawzy, Wafaa M; Elsayed, Mahmoud; Zhang, Yuchen

2013-01-01

248

Binding energies of hypernuclei and hypernuclear interactions  

International Nuclear Information System (INIS)

In part 1 the effect of nuclear core dynamics on the binding energies of ? hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the ? single-particle energy in terms of basic ?-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body ?NN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei

249

High energy theory of strong interactions  

International Nuclear Information System (INIS)

Development of strong interaction theory can be overlooked by two following supplementary directions: surveying the current theoretical approaches and models, and analysing recent experimental results. Asymptotic energies are not yet reached, polarization in pp scattering is still nonzero. Nature of the vacuum exchange (the Pomeranchuk singularity) is still an enigma. A close relationship between the t-dependent SU3-structure of the vacuum exchange and the OZI-rule regularities in the heavy meson decays, apparently, exists. This makes deeper the Regge idea on relationship of high energy behaviour and particle properties with the relevant quantum numbers. Situation with quark confinement in Dimensional Quark Counting is still puzzling. Measuring angular dependence, polarizations and phases of scattering amplitudes of the binary reactions at large angles, it is important to understand, how far are really good predictions of the Dimensional Quark Counting. Quark degrees of freedom seem to be important for a description of nucleus interactions at high energies and large transferred momenta. Presence of the fundamental length or new energy scale could change drastically the picture of particle interactions at extremal energies

250

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition.  

Science.gov (United States)

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-? interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions. PMID:25084889

Parrish, Robert M; Sherrill, C David

2014-07-28

251

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition  

Science.gov (United States)

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-? interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.

Parrish, Robert M.; Sherrill, C. David

2014-07-01

252

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

Energy Technology Data Exchange (ETDEWEB)

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 potential reproduces the crystal structure well, and is used to predict other polymorphs by a search for minima in the lattice energy. (author)

Tsui, H.H.Y

2001-07-01

253

Interactions between dark energy and dark matter  

International Nuclear Information System (INIS)

We have investigated interacting dark energy cosmologies both concerning their impact on the background evolution of the Universe and their effects on cosmological structure growth. For the former aspect, we have developed a cosmological model featuring a matter species consisting of particles with a mass that increases with time. In such model the appearance of a Growing Matter component, which is negligible in early cosmology, dramatically slows down the evolution of the dark energy scalar field at a redshift around six, and triggers the onset of the accelerated expansion of the Universe, therefore addressing the Coincidence Problem. We propose to identify this Growing Matter component with cosmic neutrinos, in which case the present dark energy density can be related to the measured average mass of neutrinos. For the latter aspect, we have implemented the new physical features of interacting dark energy models into the cosmological N-body code GADGET-2, and we present the results of a series of high-resolution simulations for a simple realization of dark energy interaction. As a consequence of the new physics, cold dark matter and baryon distributions evolve differently both in the linear and in the non-linear regime of structure formation. Already on large scales, a linear bias develops between these two components, which is further enhanced by the non-linear evolution. We also find, in contrast with previous work, that the density profiles of cold dark matter halos are less concentrated in coupled dark energy cosmologies compared with ?CDM. Also, the baryon fraction in halos in the coupled models is significantly reduced below the universal baryon fraction. These features alleviate tensions between observations and the ?CDM model on small scales. Our methodology is ideally suited to explore the predictions of coupled dark energy models in the fully non-linear regime, which can provide powerful constraints for the viable parameter space of such scenarios. (orig.)

254

Interactions between dark energy and dark matter  

Energy Technology Data Exchange (ETDEWEB)

We have investigated interacting dark energy cosmologies both concerning their impact on the background evolution of the Universe and their effects on cosmological structure growth. For the former aspect, we have developed a cosmological model featuring a matter species consisting of particles with a mass that increases with time. In such model the appearance of a Growing Matter component, which is negligible in early cosmology, dramatically slows down the evolution of the dark energy scalar field at a redshift around six, and triggers the onset of the accelerated expansion of the Universe, therefore addressing the Coincidence Problem. We propose to identify this Growing Matter component with cosmic neutrinos, in which case the present dark energy density can be related to the measured average mass of neutrinos. For the latter aspect, we have implemented the new physical features of interacting dark energy models into the cosmological N-body code GADGET-2, and we present the results of a series of high-resolution simulations for a simple realization of dark energy interaction. As a consequence of the new physics, cold dark matter and baryon distributions evolve differently both in the linear and in the non-linear regime of structure formation. Already on large scales, a linear bias develops between these two components, which is further enhanced by the non-linear evolution. We also find, in contrast with previous work, that the density profiles of cold dark matter halos are less concentrated in coupled dark energy cosmologies compared with {lambda}{sub CDM}. Also, the baryon fraction in halos in the coupled models is significantly reduced below the universal baryon fraction. These features alleviate tensions between observations and the {lambda}{sub CDM} model on small scales. Our methodology is ideally suited to explore the predictions of coupled dark energy models in the fully non-linear regime, which can provide powerful constraints for the viable parameter space of such scenarios. (orig.)

Baldi, Marco

2009-03-20

255

Energy security and climate policy. Assessing interactions  

Energy Technology Data Exchange (ETDEWEB)

World energy demand is surging. Oil, coal and natural gas still meet most global energy needs, creating serious implications for the environment. One result is that CO2 emissions, the principal cause of global warming, are rising. This new study underlines the close link between efforts to ensure energy security and those to mitigate climate change. Decisions on one side affect the other. To optimise the efficiency of their energy policy, OECD countries must consider energy security and climate change mitigation priorities jointly. The book presents a framework to assess interactions between energy security and climate change policies, combining qualitative and quantitative analyses. The quantitative analysis is based on the development of energy security indicators, tracking the evolution of policy concerns linked to energy resource concentration. The 'indicators' are applied to a reference scenario and CO2 policy cases for five case-study countries: The Czech Republic, France, Italy, the Netherlands, and the United Kingdom. Simultaneously resolving energy security and environmental concerns is a key challenge for policy makers today. This study helps chart the course.

NONE

2007-03-28

256

Intermolecular modes of solid carbon disulphide  

International Nuclear Information System (INIS)

The frequencies of particular intermolecular modes of vibration and libration in single crystal of solid carbon disulphide have been measured by coherent inelastic neutron and Raman scattering techniques at 148 K. Measurements were made at the special points in the Brillouin zone ?, S, R, Z, A, Q and Y and, including earlier infrared results, 37 of the 42 distinct frequencies at these points have been identified. Six of the ten dispersion curves along ? [001] have been measured and three dispersion curves have been outlined along ? [100]. Values of the elastic constants C11, C33, C44 and C55 have been determined from the acoustic branches. The present results are compared with calculations based on two different models for the interatomic potentials. Both models calculate the general level of the intermolecular frequencies to be too high and the bandwidth of the frequencies to be too large. Neither model can be considered an adequate description of the present results. (author)

257

Intermolecularly Hydrogen-Bonded Dimeric Helices. Tripyrrindiones  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A rare and unusual class of tripyrrolic compounds, violet-colored tripyrrin-1,14-diones, can be prepared easily and in moderately high yields from base (piperidine)-catalyzed condensation of 3-pyrrolin-2-ones with 2,5-diformylpyrroles. Dipyrrinones adopt the all syn-Z conformation leading to helical, lock-washer like structures, which form dimers that are held together by intermolecular hydrogen bonds in nonpolar solvents and in the crystal. Strong bathochromic spectral shifts of the tripyrri...

Roth, Steven D.; Shkindel, Tetyana; Lightner, David A.

2007-01-01

258

Proton-nucleus interaction at high energy  

International Nuclear Information System (INIS)

The interaction of high energy protons (between 100 MeV and 20 GeV incident energy) with nuclei is studied in the frame of an intranuclear cascade (INC) model. Particular attention is paid to the energy loss of the projectile and on the emission patterns. It is shown that, in general, the incident proton has left the nucleus before the emission process starts. The latter proceeds first on a rather short time scale and involves fast particles. Progressively the emission rate slows down and the ejected particles are less rapid. The target mass, energy and impact parameter dependences of the energy loss is displayed. As a by-product, we calculate the nuclear stopping power. We investigate the fluctuations in the number of primary collisions, i.e. those suffered by the incoming nucleon, and in the energy loss. Fluctuations in the number of ejectiles are also studied as well as the relationship between primary collisions and the number of fast (grey) particles. The latter number is tentatively related with the number of site vacancies in percolation models. The entropy created inside the target is also calculated. It is shown that the representative point of the system in the (internal energy, entropy) plane spends a relatively long time in the coexistence zone and even in the instability zone corresponding to gas-liquid transition. Implications for these two models of fragmentation are discussed. A preliminary comparison with energy loss measurements in the 3-4 GeV/c range is performed. (orig.)

259

Optimized intermolecular potential for nitriles based on Anisotropic United Atoms model.  

Science.gov (United States)

An extension of the anisotropic united atoms intermolecular potential model is proposed for nitriles. The electrostatic part of the intermolecular potential is calculated using atomic charges obtained by a simple Mulliken population analysis. The repulsion-dispersion interaction parameters for methyl and methylene groups are taken from transferable AUA4 literature parameters [Ungerer et al., J. Chem. Phys., 2000, 112, 5499]. Non-bonding Lennard-Jones intermolecular potential parameters are regressed for the carbon and nitrogen atoms of the nitrile group (-C[triple bound] N) from experimental vapor-liquid equilibrium data of acetonitrile. Gibbs Ensemble Monte Carlo simulations and experimental data agreement is very good for acetonitrile, and better than previous molecular potential proposed by Hloucha et al. [J. Chem. Phys., 2000, 113, 5401]. The transferability of the resulting potential is then successfully tested, without any further readjustment, to predict vapor-liquid phase equilibrium of propionitrile and n-butyronitrile. PMID:18478282

Hadj-Kali, Mohamed Kamel; Gerbaud, Vincent; Joulia, Xavier; Lacaze-Dufaure, Corinne; Mijoule, Claude; Ungerer, Philippe

2008-07-01

260

The geometry of the nitroguanyl fragment in the simplest nitroguanidine derivatives in the absence of intermolecular interactions: The gas electron diffraction data on 1,1,3,3-tetramethyl-2-nitroguanidine  

Science.gov (United States)

The structures and force fields of the equilibrium forms of 2-nitroguanidine ( 1), 1,1,3,3-tetramethyl-2-nitroguanidine ( 2), and nitroguanyl azide ( 3) were determined in the MP2(full)/6-311G(3 df, 2 p) approximation; wagging-inversion motions of the N amine atoms were studied. The internal rotation potential function of the NO2 group was calculated for 1. Similar functions for 1 and 2 were also obtained in the MP2(full)/6-311G( d, p) approximation. Direct one-dimensional problems for a nonrigid model were solved by the variational method, and the distribution of torsional levels was obtained. In the region of potential minimum, rotation in both molecules had the character of large-amplitude motions. For the first time, electron diffractions data were obtained at 100°C for molecule 2 without noticeable traces of substance decomposition. A structural r e analysis was performed using the model of large-amplitude motions for characteristic NO2 group torsional vibrations. Vibrational corrections to internuclear distances and mean amplitudes were calculated taking into account nonlinear kinematic effects using the force fields obtained in this work. The geometry of molecule 2 calculated in the MP2(full)/6-311G(3 df, 2 p) approximation well corresponds to the gas electron diffraction data. The parameters of molecule 2 in the crystalline phase, however, differ substantially from the parameters of the free molecule. This corresponds with the suggestion of the influence of intermolecular H-bonds involving the imine nitrogen atom and nitro groups oxygen atoms.

Khaikin, L. S.; Grikina, O. E.; Girichev, G. V.; Kovacs, A.; Dyugaev, K. P.; Astachov, A. M.

2011-03-01

 
 
 
 
261

SCF and CI potential energy curves for H2-H2+ interactions  

International Nuclear Information System (INIS)

Potential energy curves have been computed using SCF and CI techniques for ground and excited state interactions of H2 with H2+. A total of seven planar and two nonplanar interaction geometries have been studied. In all cases the H2 and H2+ bond lengths were restricted to their equilibrium values, while the intermolecular H2-H2+ distance varied from 0.5 to 12 au. Ground state binding energies were found to range from 0.4 to 1.6 eV in the SCF calculations and from 0.8 to 1.9 eV in the complete single-and-double excitation CI calculations (SD-CI). In both SCF and SD-CI calculations, the most stable geometry was found to be the perpendicular orientation, with the H2+ molecule lying on a line bisecting the H2 bond axis. Potential curves were also computed for the charge-transfer excited state of H2-H+2, and these results are discussed in terms of their implications for the dynamics of charge exchange reactions

262

Strongly Interacting Matter at High Energy Density  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This lecture concerns the properties of strongly interacting matter (which is described by Quantum Chromodynamics) at very high energy density. I review the properties of matter at high temperature, discussing the deconfinement phase transition . At high baryon density and low temperature, large $N_c$ arguments are developed which suggest that high baryonic density matter is a third form of matter, Quarkyonic Matter, that is distinct from confined hadronic matter and deconfi...

Mclerran, Larry

2008-01-01

263

Nuclear Self-energy and Realistic Interactions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The structure of nucleon self-energy in nuclear matter is evaluated for various realistic models of the nucleon-nucleon (NN) interaction. Starting from the Brueckner-Hartree-Fock approximation without the usual angle-average approximation, the effects of hole-hole contributions and a self-consistent treatment within the framework of the Green function approach are investigated. Special attention is paid to the predictions for the spectral function originating from various mo...

Frick, T.; Gad, Kh; Mu?ther, H.; Czerski, P.

2001-01-01

264

Interactions of quarkonium at low energies  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present two examples of the short-distance QCD calculations for the quarkonium (\\Phi) interactions; 1) \\pi \\Phi elastic and \\pi \\Phi -> \\pi \\Phi' cross sections, and 2) the potential between two \\Phi's. The former is relevant for the \\Phi suppression in heavy ion collisions; we find that the corresponding cross sections are very small. For the latter we derive the sum rule which relates the strength of the potential to the energy density of the QCD vacuum. The key startin...

Fujii, H.; Kharzeev, D.

1999-01-01

265

Low Energy Pion-Hyperon Interaction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We study the low energy pion-hyperon interaction considering effective non-linear chiral invariant Lagrangians including pions, rho mesons, hyperons and corresponding resonances. Then we calculate the S- and P-wave phase-shifts, total cross sections, angular distributions and polarizations for the momentum in the center-of-mass frame up to k=400 MeV. With these results we discuss the CP violation in the csi-> pi-lambda and omega-> pi-csi weak decays.

Junior, Celso Camargo Barros; Hama, Yogiro

2000-01-01

266

Redshift drift exploration for interacting dark energy  

CERN Document Server

By detecting redshift drift in the spectra of Lyman-$\\alpha$ forest of distant quasars, Sandage-Loeb (SL) test directly measures the expansion of the universe, covering the "redshift desert" of $2 \\lesssim z \\lesssim5$. Thus this method is definitely an important supplement to the other geometric measurements and will play a crucial role in cosmological constraints. In this paper, we quantify the ability of SL test signal by a CODEX-like spectrograph for constraining interacting dark energy. Four typical interacting dark energy models are considered: (\\romannumeral1) $Q=\\gamma H\\rho_c$, (\\romannumeral2) $Q=\\gamma H\\rho_{de}$, (\\romannumeral3) $Q=\\gamma H_0\\rho_c$, and (\\romannumeral4) $Q=\\gamma H_0\\rho_{de}$. The results show that for all the considered interacting dark energy models, relative to the current joint SN+BAO+CMB+$H_0$ observations, the constraints on $\\Omega_m$ and $H_0$ would be improved by about 60\\% and 30--40\\%, while the constraints on $w$ and $\\gamma$ would be slightly improved, with a 30-y...

Geng, Jia-Jia; Zhang, Jing-Fei; Zhang, Xin

2015-01-01

267

A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints  

International Nuclear Information System (INIS)

A simple and reliable approach for docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints (as few as three from a single point) in combination with a novel representation for an attractive potential between mapped interaction surfaces is described. Unambiguous assignments of very sparse intermolecular NOEs are obtained using a reverse labeling strategy in which one the components is fully deuterated with the exception of selective protonation of the ?-methyl groups of isoleucine, while the other component is uniformly 13C-labeled. This labeling strategy can be readily extended to selective protonation of Ala, Leu, Val or Met. The attractive potential is described by a 'reduced' radius of gyration potential applied specifically to a subset of interfacial residues (those with an accessible surface area ? 50% in the free proteins) that have been delineated by chemical shift perturbation. Docking is achieved by rigid body minimization on the basis of a target function comprising the sparse NOE distance restraints, a van der Waals repulsion potential and the 'reduced' radius of gyration potential. The method is demonstrated for two protein-protein complexes (EIN-HPr and IIAGlc-HPr) from the bacterial phosphotransferase system. In both cases, starting from 100 different random orientations of the X-ray structures of the free proteins, 100% convergence is achieved to a single cluster (with near identical atosingle cluster (with near identical atomic positions) with an overall backbone accuracy of ?2 A. The approach described is not limited to NMR, since interfaces can also be mapped by alanine scanning mutagenesis, and sparse intermolecular distance restraints can be derived from double cycle mutagenesis, cross-linking combined with mass spectrometry, or fluorescence energy transfer

268

The role of intermolecular interactions in the assemblies of FeII and CoII tetrakis-isothiocyanatometalates with tris(1,10-phenanthroline)-RuII: Crystal structures of two dual-metal assemblies featuring octahedral cationic and tetrahedral anionic modules  

International Nuclear Information System (INIS)

Two new dual-metal assemblies: 2[Ru(phen)3]2+.[Fe(SCN)4]2-.2SCN-.4H2O 1 and [Ru(phen)3]2+.[Co(SCN)4]2-2, (phen:1,10-phenanthroline), have been prepared and their structures were characterized by X-ray diffraction. In 1, the cationic octahedral enantiomers are arranged with a ????? sequence supported by ?-? stacking and the anionic inorganic tetrahedral units are oriented between these stacks by interacting with the nearby water molecules through strong O-H...O and O-H...S hydrogen bonds. In 2, homochiral double helices in the b-direction are revealed, with tetrakis-isothiocyanate CoII anions arranged in the crystal to furnish one-dimensional (1D)-helical chains with S...S intermolecular interactions at 3.512(2) and 3.966(2) A supporting [Ru(phen)3]2+?- and ?-helices with Ru...Ru shortest distance of 8.676(7) A. In both 1 and 2, the supramolecular assembly is maintained by C-H...S hydrogen bonds extending between the phenanthroline aromatic carbons in the cationic nodes and the sulphur atoms of the isothiocyanates anions. Analysis of S...S interactions in isothiocyanate containing compounds using Cambridge structural database (CSD) showed an angle dependence categorizing these interactions into 'type-I' and 'type-II'. - Graphical abstract: Side projection in 2 showing the crankshaft caused by S...S interactions in [Co(Ned by S...S interactions in [Co(NCS)4]2- in-between [RuII(phen)3]2+ helices. Only isothiocyanates arms of [Co(NCS)4]2- that are part of S...S interactions are shown and [RuII(phen)3]2+ are presented as polyhedra

269

Direct detection of intermolecular forces by atomic force microscopy  

Science.gov (United States)

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

Skulason, Hjalti

270

The NN and NY Interactions at Small Energies  

Science.gov (United States)

We discuss recent results and open problems in baryon-baryon interactions at small relative energies. Here we concentrate on pp and pn final state interactions in pion production reactions and on ?p interactions in kaon production.

Machner, Hartmut; Hinterberger, Frank; Siudak, Regina

271

A new intermolecular mechanism to selectively drive photoinduced damages  

CERN Document Server

Low-energy electrons (LEEs) are known to be effective in causing strand breaks in DNA. Recent experiments show that an important direct source of LEEs is the intermolecular Coulombic decay (ICD) process. Here we propose a new cascade mechanism initiated by core excitation and terminated by ICD and demonstrate its properties. Explicit calculations show that the energies of the emitted ICD-electrons can be controlled by selecting the initial atomic excitation. The properties of the cascade may have interesting applications in the fields of electron spectroscopy and radiation damage. Initiating such a cascade by resonant X-ray absorption from a high-Z element embedded in a cancerous cell nucleus, ICD will deliver genotoxic particles \\textit{locally} at the absorption site, increasing in that way the controllability of the induced damage.

Gokhberg, Kirill; Kuleff, Alexander I; Cederbaum, Lorenz S

2014-01-01

272

Dark matter interacts with variable vacuum energy  

Science.gov (United States)

We investigate a spatially flat Friedmann-Robertson-Walker scenario with two interacting components, dark matter and variable vacuum energy densities, plus two decoupled components, one is a baryon term while the other behaves as a radiation component. We consider a linear interaction in the derivative dark component density. We apply the method to the observational Hubble data for constraining the cosmological parameters and analyze the amount of dark energy in the radiation era for the model. It turns out that our model fulfills the severe bound of at level, so is consistent with the recent analysis that include cosmic microwave background anisotropy measurements from Planck survey, the future constraints achievable by Euclid and CMBPol experiments, reported for the behavior of the dark energy at early times, and fulfills the stringent bound at level in the big-bang nucleosynthesis epoch. We also examine the cosmic age problem at high redshift associated with the old quasar APM 08279+5255 and estimate the age of the universe today.

Sánchez G., Iván E.

2014-08-01

273

Dark matter interacts with variable vacuum energy  

CERN Document Server

We investigate a spatially flat Friedmann-Robertson-Walker (FRW) scenario with two interacting components, dark matter and variable vacuum energy (VVE) densities, plus two decoupled components, one is a baryon term while the other behaves as a radiation component. We consider a linear interaction in the derivative dark component density. We apply the $\\chi^2$ method to the observational Hubble data for constraining the cosmological parameters and analyze the amount of dark energy in the radiation era for the model. It turns out that our model fulfills the severe bound of $\\Omega_{x}(z\\simeq 1100)<0.009$ at $2\\sigma$ level, so is consistent with the recent analysis that includes cosmic microwave background anisotropy measurements from Planck survey, the future constraints achievable by Euclid and CMBPol experiments, reported for the behavior of the dark energy at early times, and fulfills the stringent bound $\\Omega_{x}(z\\simeq 10^{10})<0.04$ at $2\\sigma$ level in the big-bang nucleosynthesis epoch. We a...

G, Iván E Sánchez

2014-01-01

274

Nano-spectroscopic imaging of intermolecular structure, coupling and dynamics  

CERN Document Server

Molecular self-assembly, the function of biomembranes, and the performance of organic solar cells rely on molecular interactions on the nanoscale. The understanding and design of such intrinsic or engineered heterogeneous functional soft matter has long been impeded by a lack of spectroscopic tools with sufficient nanometer spatial resolution, attomolar sensitivity, and intermolecular spectroscopic specificity. We implement vibrational scattering-scanning near-field optical microscopy ($s$-SNOM) in a multi-spectral modality with unprecedented spectral precision to investigate the structure-function relationship in nano-phase separated block-copolymers. We use a vibrational resonance as a sensitive reporter of the local chemical environment and resolve, with few nanometer spatial resolution and 0.2 cm$^{-1}$ spectral precision, spectral Stark shifts and line broadening correlated with molecular-scale morphologies. By creating images of solvatochromic vibrational shifts we discriminate local variations in elect...

Pollard, Benjamin; Hinrichs, Karsten; Raschke, Markus B

2013-01-01

275

[High-energy electron-positron interactions  

International Nuclear Information System (INIS)

The purpose of the research was the study of electron-positron interactions at high energies using the Time Projection Chamber (TPC) at the Positron Electron Project (PEP) at SLAC. The TPC detector had an initial data gathering from 1982 until 1986 and accumulated a data sample with an integrated luminosity of -150 pb-1 at an electron-positron energy of 29 GeV. The data runs in the 1988--1990 time period (yielding ? pb-1) were abbreviated, due to the need of the laboratory to give highest priority to the new Stanford Linear Collider (SLC). The TPC collaboration decided in 1991 to discontinue data taking, but has continued the collaboration for the purpose of completing the analysis of the data. When UMass joined the SLD project, it was being designed as a new state-of-the-art detector for studying electron-positron interactions at energies in the vicinity of 91 GeV, the Z0 mass. The detector was completed and installed at the interaction point of the SLC in 1991, at which time an initial, ''engineering run'' allowed the debugging of detector components and provided a data sample of ?1,000 events with hadronic Z0 decays. In 1992 the SLC provided beams of polarized electrons and the SLD collected a data sample in excess of 11,000 hadronic Z0 events produced by polarized electrons, allowing unique measurements of some of the parameters of the standard model. This project is continuing to take data in 1993 with increased polarization and higher luminosity. This report reviews the research work performed under the contract, and survey's the physics results

276

Weak interactions at high energies. [Lectures, review  

Energy Technology Data Exchange (ETDEWEB)

Review lectures are presented on the phenomenological implications of the modern spontaneously broken gauge theories of the weak and electromagnetic interactions, and some observations are made about which high energy experiments probe what aspects of gauge theories. Basic quantum chromodynamics phenomenology is covered including momentum dependent effective quark distributions, the transverse momentum cutoff, search for gluons as sources of hadron jets, the status and prospects for the spectroscopy of fundamental fermions and how fermions may be used to probe aspects of the weak and electromagnetic gauge theory, studies of intermediate vector bosons, and miscellaneous possibilities suggested by gauge theories from the Higgs bosons to speculations about proton decay. 187 references. (JFP)

Ellis, J.

1978-08-01

277

Customers' Interaction in Super Distributed Energy Systems  

Science.gov (United States)

This paper deals with numerical analysis of behaviors for cooperative and competitive systems operated in the super distributed environment. Since the behavior is dictated by a complicated interaction of electric power outputs produced by numerous dispersed generators, the study is focused on the macroscopic behavior as well as the microscopic behavior of numerous dispersed generators based on the stability analysis of the Hopfield neural network. Some simulation results using a typical energy system model make it clear that maintenance of supply-and-demand balance becomes difficult when customers with a dispersed generation system cannot obtain sufficient information from their neighborhood.

Ishii, Tsunayoshi; Yasuda, Keiichiro

278

High energy photon-neutrino interactions  

International Nuclear Information System (INIS)

A general decomposition of the amplitudes for the 2 ? 2 processes ?? ? ?? and ?? ? ? bar ? is obtained using gauge invariance and Bose symmetry. The restrictions implied by this decomposition are investigated for the reaction ?? ? ? bar ? by computing the one-loop helicity amplitudes in the standard model. In the center of mass, where ?s = 2?, the cross section grows roughly as ?6 up to the threshold for W-boson production, ?s 2mW. Astrophysical implications of very high energy photon-neutrino interactions are discussed

279

Interaction between Dark Energy and Dark Matter Crosses Non-interacting Line  

CERN Document Server

It is found by Cai and Su that the interaction between dark energy and cold dark matter is likely to cross the non-interacting line. Motivated by this, we suggest a form of interaction between dark energy and dark matter, which changes from negative to positive as our universe changing from deceleration to acceleration. It is found that the interaction is favored by the second law of thermodynamics. Furthermore, we apple the interaction to the interacting holographic dark energy model. We find that the interacting model works well.

Sun, Cheng-Yi

2012-01-01

280

Intermolecular structure factors of macromolecules in solution : integral equation results  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The intermolecular structure of semidilute polymer solutions is studied theoretically. The low-density limit of a generalized Ornstein Zernicke integral equation approach to polymeric liquids is considered. Scaling laws for the dilute-to-semidilute crossover of the random-phase approximation (RPA)-like structure are derived for the intermolecular structure factor on large distances when intermolecular excluded volume is incorporated at the microscopic level. This leads to a nonlinear equation...

Fuchs, Matthias; Mu?ller, M.

1999-01-01

 
 
 
 
281

IMPROPER HYDROGEN BONDS - A THEORETICAL STUDY ABOUT THE MOLECULAR STRUCTURE OF INTERMOLECULAR SYSTEMS FORMED BY H3C-H+?...X AND H3C+?...H-Y WITH X = CL- OR F- AND Y = CL OR F  

Directory of Open Access Journals (Sweden)

Full Text Available In this work is presented a theoretical study of the molecular properties of the H3C-H...X and H3C+?...H-Y intermolecular systems with X = CL- or F- and Y = Cl or F. In the H3C-H...X complex, it is formed a traditional hydrogen bond between the CL- or F- anions and the hydrogen atom of the methyl. About the H3C+?...H-Y complex, it was observed an improper hydrogen bond because the carbon atom of the methyl cation function as a proton acceptor. In this insight, the capacity of methane to interact with halogen anions (CL- or F- and molecular acids (HCl or HF was examined at the B3LYP/6-311++G(3df,3dp level of calculation. Moreover, the interaction strengths of the H3C-H...X and H3C+?...H-Y complexes was evaluated by computing their intermolecular distances and binding energies. Finally, QTAIM calculations also were executed with the purpose to examine the intermolecular interactions through the quantification of their electronic densities (p as well as by the interpretation of the Laplacian operators (.

B.G OLIVEIRA

2009-01-01

282

Interacting dark energy with inhomogeneous equation of state  

Energy Technology Data Exchange (ETDEWEB)

We have investigated the model of dark energy interacting with dark matter by choosing inhomogeneous equations of state for the dark energy and a nonlinear interaction term for the underlying interaction. The equations of state have dependencies either on the energy densities, the redshift, the Hubble parameter or the bulk viscosity. We have considered these possibilities and have derived the effective equations of state for the dark energy in each case. (orig.)

Jamil, Mubasher; Rashid, Muneer Ahmad [National University of Sciences and Technology, Center for Advanced Mathematics and Physics, Rawalpindi (Pakistan)

2008-08-15

283

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  

Energy Technology Data Exchange (ETDEWEB)

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.

Grimes, R.M.

1986-11-01

284

An Intermolecular Vibration Model for Lattice Ice  

Directory of Open Access Journals (Sweden)

Full Text Available Lattice ice with tetrahedral arrangement is studied using a modified Einstein’s model that incorporates the hindered translational and rotational vibration bands into a harmonic oscillation system. The fundamental frequencies for hindered translational and rotational vibrations are assigned based on the intermolecular vibration bands as well as thermodynamic properties from existing experimental data. Analytical forms for thermodynamic properties are available for the modified model, with three hindered translational bands at (65, 229, 229 cm-1 and three effective hindered rotational bands at 560 cm-1. The derived results are good for temperatures higher than 30 K. To improve the model below 30 K, Lorentzian broadening correction is added. This simple model helps unveil the physical picture of ice lattice vibration behavior.

Quinn M. Brewster

2010-06-01

285

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

Science.gov (United States)

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

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

2014-07-10

286

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods.  

Science.gov (United States)

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (?E(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-? quality. Computed total ?E(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects. PMID:21842894

Antony, Jens; Grimme, Stefan; Liakos, Dimitrios G; Neese, Frank

2011-10-20

287

Scattering with absorptive interaction: Energy-dependent potentials  

International Nuclear Information System (INIS)

The energy dependence and analytic structure of the effective interaction for elastic scattering of composite particles are investigated using Feshbach's projection technique. A generalized Levinson theorem is established for complex, nonlocal, and energy-dependent interactions. The analytical results are illustrated by means of Argand diagrams for a solvable model and the effect of energy-averaging is discussed

288

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

Science.gov (United States)

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

Du, Xuezhong; Liang, Yingqiu

2004-01-01

289

Structure determination of three furan-substituted benzimidazoles and calculation of ?-? and C-H···? interaction energies.  

Science.gov (United States)

The synthesis and structural characterization of 2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzimidazole [C16H12N2O2, (I)], 2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzimidazol-3-ium chloride monohydrate [C16H13N2O2(+)·Cl(-)·H2O, (II)] and the hydrobromide salt 5,6-dimethyl-2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzimidazol-3-ium bromide [C18H17N2O2(+)·Br(-), (III)] are described. Benzimidazole (I) displays two sets of aromatic interactions, each of which involves pairs of molecules in a head-to-tail arrangement. The first, denoted set (Ia), exhibits both intermolecular C-H···? interactions between the 2-(furan-2-yl) (abbreviated as Fn) and 1-(furan-2-ylmethyl) (abbreviated as MeFn) substituents, and ?-? interactions involving the Fn substituents between inversion-center-related molecules. The second, denoted set (Ib), involves ?-? interactions involving both the benzene ring (Bz) and the imidazole ring (Im) of benzimidazole. Hydrated salt (II) exhibits N-H···OH2···Cl hydrogen bonding that results in chains of molecules parallel to the a axis. There is also a head-to-head aromatic stacking of the protonated benzimidazole cations in which the Bz and Im rings of one molecule interact with the Im and Fn rings of adjacent molecules in the chain. Salt (III) displays N-H···Br hydrogen bonding and ?-? interactions involving inversion-center-related benzimidazole rings in a head-to-tail arrangement. In all of the ?-? interactions observed, the interacting moieties are shifted with respect to each other along the major molecular axis. Basis set superposition energy-corrected (counterpoise method) interaction energies were calculated for each interaction [DFT, M06-2X/6-31+G(d)] employing atomic coordinates obtained in the crystallographic analyses for heavy atoms and optimized H-atom coordinates. The calculated interaction energies are -43.0, -39.8, -48.5, and -55.0?kJ?mol(-1) for (Ia), (Ib), (II), and (III), respectively. For (Ia), the analysis was used to partition the interaction energies into the C-H···? and ?-? components, which are 9.4 and 24.1?kJ?mol(-1), respectively. Energy-minimized structures were used to determine the optimal interplanar spacing, the slip distance along the major molecular axis, and the slip distance along the minor molecular axis for 2-(furan-2-yl)-1H-benzimidazole. PMID:25471412

Geiger, David K; Geiger, H Cristina; Deck, Jared M

2014-12-01

290

Study of Intermolecular Interactions of Binary Liquid Mixtures by Measuring Intensive Macroscopic Properties at (303.15, 313.15 and 323.15 K and at Ambient Pressure  

Directory of Open Access Journals (Sweden)

Full Text Available Measurements of thermodynamic and transport properties have been adequately employed in understanding the nature of molecular systems and physico-chemical behavior in liquid mixtures. These properties are important from practical and theoretical point of view to understand liquid theory. In the present study density (? and viscosity (?, have been measured for a binary liquid mixture of Diacetone alcohol with benzene and chlorobenzene, over the entire composition range at 303.15 K, 313.15 K and 323.15 K and the evaluation of different excess properties. The viscosity values and excess values were fitted to respective models. It was found that in all cases, the data obtained fitted with the values correlated by the corresponding models very well. The molecular interactions existing between the components and comparison of liquid mixtures were also discussed.

T.R Kubendran

2009-02-01

291

Resonant Auger decay driving intermolecular Coulombic decay in molecular dimers  

Science.gov (United States)

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

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

2014-01-01

292

Insight into the modified Ibalizumab-human CD4 receptor interactions: using a computational binding free energy approach.  

Science.gov (United States)

Antibody drugs are very useful tools for the treatment of many chronic diseases. Recently, however, patients and doctors have encountered the problem of drug resistance. How to improve the affinity of antibody drugs has therefore become a pressing issue. Ibalizumab is a humanized monoclonal antibody that binds human CD4, the primary receptor for human immunodeficiency virus type 1. This study investigates the mutation residues of the complementarity determining regions of Ibalizumab. We propose using the wild and mutations of Ibalizumab-human CD4 receptor complex structures, molecular dynamics techniques, alanine-scanning mutagenesis calculations and solvated interaction energies methods to predict the binding free energy of the Ibalizumab-human CD4 receptor complex structures. This work found that revealed three key positions (31th, 32th and 33th in HCDR-1) of the residues may play an important role in Ibalizumab-human CD4 receptor complex interactions. Therefore, bioengineering substitutions of the three key positions and increasing number of intermolecular interactions (HCDR-1 of Ibalizumab/human CD4 receptor) might improve the binding affinities of this complex structure. PMID:25342515

Wang, Yeng-Tseng; Chuang, Lea-Yea

2015-01-01

293

When do we need attractive-repulsive intermolecular potentials?  

Science.gov (United States)

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

Venkattraman, Ayyaswamy

2014-12-01

294

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

Science.gov (United States)

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

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

2014-12-01

295

Virtual photon interactions in high energy QCD  

International Nuclear Information System (INIS)

We study the interactions of virtual photons in the high energy limit of quantum chromodynamics (QCD). The subject is discussed in terms of two closely linked applications: the calculation of the total cross section for ?*?*-scattering and the description of DIS in the colour dipole model. We calculate virtual corrections in ?s to the process ?* q ? (qq)q and the tree level process ?* q ? (qqg)q in the high energy limit. From this calculation we obtain one-loop corrections to the effective ?*-reggeon-qq-vertex in the helicity basis of the virtual photon and the qq-pair. The loop integrals for the virtual corrections have been performed and expressed in dimensional regularization in terms of logarithms and dilogarithms. We have convoluted the virtual one-loop matrix elements with tree level matrix elements and expressed the integrals over the phase space of the qq-pair explicitly in terms of a set of standard integrals. The real corrections have been calculated and, in case of the longitudinal polarization, expressed in factorized form. From these calculations, the impact factor of virtual photons will be determined, allowing for a first prediction of the total cross section for ?*?*-scattering in the next-to-leading-log s approximation. The calculations in this thesis extend the photon wave function picture in the colour dipole model to next-to-leading order. For this pt-to-leading order. For this purpose, the real corrections with a qqg final state are analyzed in transverse configuration space and interpreted as a first higher Fock component of the photon wave function. In addition, the matrix elements that have been calculated in this thesis are needed for the calculation of jet cross sections. (orig.)

296

Reconstruction of interacting dark energy models from parameterizations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Models with interacting dark energy can alleviate the cosmic coincidence problem by allowing dark matter and dark energy to evolve in a similar fashion. At a fundamental level, these models are specified by choosing a functional form for the scalar potential and for the interaction term. However, in order to compare to observational data it is usually more convenient to use parameterizations of the dark energy equation of state and the evolution of the dark matter energy den...

Rosenfeld, Rogerio

2007-01-01

297

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

International Nuclear Information System (INIS)

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 experimene 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 potential reproduces the crystal structure well, and is used to predict other polymorphs by a search for minima in the lattice energy. (author)

298

Cosmography of interacting generalized QCD ghost dark energy  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Exploring the accelerated expansion of the universe, we investigate the generalized ghost dark energy (GGDE) model from the statefinder diagnosis analysis in a flat FRW universe. First we calculate the cosmological evolution and statefinder trajectories for non-interacting case and then extend this work by considering the interaction between dark matter and dark energy components. We show that in the non-interacting case the phantom line can not be crossed and also he evolut...

Malekjani, Mohammad

2012-01-01

299

Analytical and Numerical Calculations of Diffusion Effects on the Intermolecular Multiple Quantum Coherences in Solution NMR  

International Nuclear Information System (INIS)

We calculated the analytical solutions to evaluate the effects of diffusion on the iMQCs in CRAZED pulse sequences. The obtained solution has been verified using the results of numerical simulation. The diffusional behaviors of the iMQCs during both the evolution and detection time periods could be examined by the analytical solution, which was quite different from those of the conventional NMR experiments. Understanding the difference in diffusional behaviors could lead to useful applications such as diffusion MRI based on the detection of iMQCs. The intermolecular multiple quantum coherences (iMQCs) that are generated by intermolecular dipolar interactions between distant spins on different molecules, have recently gained considerable attention because their properties are intrinsically different from those of conventional single quantum coherences (SQCs) in solution NMR. This feature allows for a wider range of applications in NMR and MR imaging

300

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

Science.gov (United States)

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

Chaudhari, Sachin Rama; Suryaprakash, N.

2012-05-01

 
 
 
 
301

Analytical and Numerical Calculations of Diffusion Effects on the Intermolecular Multiple Quantum Coherences in Solution NMR  

Energy Technology Data Exchange (ETDEWEB)

We calculated the analytical solutions to evaluate the effects of diffusion on the iMQCs in CRAZED pulse sequences. The obtained solution has been verified using the results of numerical simulation. The diffusional behaviors of the iMQCs during both the evolution and detection time periods could be examined by the analytical solution, which was quite different from those of the conventional NMR experiments. Understanding the difference in diffusional behaviors could lead to useful applications such as diffusion MRI based on the detection of iMQCs. The intermolecular multiple quantum coherences (iMQCs) that are generated by intermolecular dipolar interactions between distant spins on different molecules, have recently gained considerable attention because their properties are intrinsically different from those of conventional single quantum coherences (SQCs) in solution NMR. This feature allows for a wider range of applications in NMR and MR imaging.

Chung, Keechoo; Jin, Gyungsu; Won, Daeun; Chang, Sukkyu; Ahn, Sangdoo [Chung-Ang Univ., Seoul (Korea, Republic of); Hwang, Su Jung; Cho, Jeehyun [Korea Basic Science Institute, Ochang (Korea, Republic of)

2013-12-15

302

Long-range intermolecular dispersion forces and circular dichroism spectra from first-principles calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules and of electronic circular dichroism spectra of chiral molecules. The former is expressed in terms of the C6 dipole-dipole dispersion coefficients ??, and the latter is given in terms of the extinction coefficient. In a series of publications, the complex linear polarization propagator method has been shown to be a powerful tool to provide accurate ab initio and f...

Jiemchooroj, Auayporn

2007-01-01

303

Intermolecular Cope-type hydroamination of alkynes using hydrazines.  

Science.gov (United States)

Metal-free, intermolecular hydroaminations are performed upon heating aryl acetylenes and MeNHNH(2) at 140 degrees C, with preferential formation of the linear, "anti-Markovnikov" hydrazones. PMID:18188478

Cebrowski, Pamela H; Roveda, Jean-Grégoire; Moran, Joseph; Gorelsky, Serge I; Beauchemin, André M

2008-01-28

304

Computational estimation of specific side chain interaction energies in ? helices  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have used a structure energy-based computer program developed for protein design, Perla, to provide theoretical estimates of all specific side chain–side chain interaction energies occurring in ? helices. The computed side chain–side chain interaction energies were used as substitutes for the corresponding values used by the helix/coil transition algorithm, AGADIR. Predictions of peptide helical contents were nearly as successful as those obtained with the originally calibrated set of...

Fisinger, Samo; Serrano, Luis; Lacroix, Emmanuel

2001-01-01

305

Tuning Aryl?CH···O Intermolecular Interactions on Pt(111)  

DEFF Research Database (Denmark)

Scanning tunneling microscopy (STM) data are reported for the room-temperature adsorption of 2,2,2-trifluoroacetophenone (TFAP), 2,2,2-trifluorovinylbenzene (TFVB), octafluoroacetophenone (OFAP), and methyl benzoate (MB) on Pt(111). The objective of the study is to establish the role of aryl?CH···O bonding in forming self-assembled low-nuclearity structures at room temperature and to compare aryl?CH···O bonding by ester and ketone carbonyl functions. The STM images clearly evidence the formation of homochiral dimers and trimers of TFAP, and density functional theory (DFT) calculations reveal aryl?CH···O bonding as the driving force for dimer formation. In contrast to TFAP, chemisorbed TFVB and OFAP do not form such self-assembled structures as they lack carbonyl and aryl?CH groups, respectively. The self-assembly of MB on Pt(111) differs from that of TFAP, in that it can form structures stabilized by one, as distinct from two, aryl?CH···O bonds. The results are discussed with respect to the enantioselective hydrogenation of ?-ketoesters on cinchona modified Pt catalysts.

Demers-Carpentier, Vincent; Laliberte, Marc-Andre?

2011-01-01

306

Study of intermolecular interactions by matrix isolation vibrational spectroscopy  

International Nuclear Information System (INIS)

The application of matrix isolation infrared and Raman spectroscopy to the study of the self-association of hydrogen bonding substances is discussed. The use of the technique to elucidate the structures of small multimer species of hydrogen chloride, hydrogen cyanide, water and ammonia is described. The results of far infrared spectral studies enable some of the hydrogen bond stretching and bending modes of these species to be identified. Matrix spectra of the pyridine-hydrogen chloride complex are also discussed. (orig.)

307

Proinsulin intermolecular interactions during secretory trafficking in pancreatic ? cells.  

Science.gov (United States)

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

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

2013-01-18

308

Proton-nuclei interactions at high energies  

International Nuclear Information System (INIS)

Hadron-Nucleus interactions has been playing an important role in nuclear physics for last five decades. Several experimental techniques have been demonstrated for hadron-nucleus absorption cross-sections of charged Pions, charged Kaons, protons, and antiprotons on several target nuclei. Many theoretical models have been proposed for the study of such interactions. In the present paper only one hadron (i.e. proton) has been included in the study. In this work a universal approach has been proposed to calculate the absorption cross-sections for proton interacting with target nuclei. The cross sections represented is in the unit of milli barn (mb) in this paper

309

New Molecular Collisional Interaction Effect in Low-Energy Sputtering  

Science.gov (United States)

An unexpected pronounced enhancement is observed in sputtering yields per atom for N+2 compared to N+ from a polycrystalline gold target. This effect is seen when the kinetic energy per projectile atom is below 500 eV and increases as projectile energy decreases to near-threshold energies. Enhancements for O+2 over O+ begin at even lower kinetic energies below 100 eV per atom. This new molecular interaction effect may be explained qualitatively by invoking a simple energy transfer model which involves the vibrational frequency of the molecule and the collisional interaction time.

Yao, Y.; Hargitai, Z.; Albert, M.; Albridge, R. G.; Barnes, A. V.; Gilligan, J. M.; Pratt Ferguson, B.; Lüpke, G.; Gordon, V. D.; Tolk, N. H.; Tully, J. C.; Betz, G.; Husinsky, W.

1998-07-01

310

Intermolecular spin-spin coupling in highly fluorinated solutions of galvinoxyl free radical  

International Nuclear Information System (INIS)

The Overhauser effect type dynamic nuclear polarization experiments were performed to study the solutions of the stable free radical Galvinoxyl in highly fluorinated aliphatic and aromatic solvents. Mainly the Overhauser effect, which normally arises due to both dipolar and scalar interactions between the unpaired electrons of the free radical molecules and fluorine nuclei of solvent molecules, occurs in the solutions, which are examined in this study. As solvent, N-Methyl-bis-trifluoroacetamide and Octafluorotoluene were used. The experiments were performed at a low field double resonance NMR spectrometer, which operates at 1.53 mT. The NMR enhancements depend on competition between intermolecular magnetic interactions. We investigated the NMR enhancement factors depending to the ESR frequency, which is modulated by the interaction between the electron spin of the free radical and nuclear spins in its vicinity, at four different temperatures. It was found that the electron spin of the free radical interact very strongly with the nitrogen atom of the N-Methyl-bistrifluoroacetamide molecule rather than hydrogen atoms of own radical molecule. Galvinoxyl free radical doesn't show this interaction with the other solvents at the weak field. This effect, which has been reported as an intramolecular interaction previously, is observed first time as an intermolecular coupling in this study.

311

Cosmological Evolution With Interaction Between Dark Energy And Dark Matter  

CERN Document Server

In this review we consider in detail different theoretical topics associated with interaction in the dark sector. We study linear and nonlinear interactions which depend on the dark matter and dark energy densities. We consider a number of different models (including the holographic dark energy and dark energy in a fractal universe) with interacting dark energy (DE) and dark matter (DM), have done a thorough analysis of these models. The main task of this review was not only to give an idea about the modern set of different models of dark energy, but to show how much can be diverse dynamics of the universe in these models. We find that the dynamics of a Universe that contains interaction in the dark sector can differ significantly from the Standard Cosmological Model (SCM).

Bolotin, Yu L; Lemets, O A; Yerokhin, D A

2013-01-01

312

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

Science.gov (United States)

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

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

2014-10-13

313

Load Matching and Grid Interaction of Net Zero Energy Buildings  

DEFF Research Database (Denmark)

“Net Zero Energy Building” has become a prominent wording to describe the synergy of energy efficient building and renewable energy utilization to reach a balanced energy budget over a yearly cycle. Taking into account the energy exchange with a grid infrastructure overcomes the limitations of seasonal energy storage on-site. Even though the wording “Net Zero Energy Building” focuses on the annual energy balance, large differences may occur between solution sets in the amount of grid interaction needed to reach the goal. The paper reports on the analysis of example buildings concerning the load matching and grid interaction. Indices to describe both issues are proposed and foreseen as part of a harmonized definition framework. The work is part of subtask A of the IEA SHCP Task40/ECBCS Annex 52: “Towards Net Zero Energy Solar Buildings”.

Voss, Karsten; Sartori, Igor

2010-01-01

314

The distinguishability of interacting dark energy from modified gravity  

International Nuclear Information System (INIS)

We study the observational viability of coupled quintessence models with their expansion and growth histories matched to modified gravity cosmologies. We find that for a Dvali-Gabadadze-Porrati model which has been fitted to observations, the matched interacting dark energy models are observationally disfavoured. We also study the distinguishability of interacting dark energy models matched to scalar-tensor theory cosmologies and show that it is not always possible to find a physical interacting dark energy model which shares their expansion and growth histories

315

Interaction energy between a positronium atom and a metal surface  

International Nuclear Information System (INIS)

The interaction energy of a positronium atom interacting with a metal surface is obtained as a function of the speed of the positronium atom and the separation from the metal surface. It is shown that the energy saturates to a finite value at the surface and follows the Lifshitz relation for large separations. The treatment is based on the consideration of the virtual excitations of the multipoles of the atom, while in the earlier work by Manson and Ritchie only the dipolar excitations were considered. The divergence of the interaction energy obtained by the earlier authors arises due to incomplete consideration of multipolar effects

316

The distinguishability of interacting dark energy from modified gravity  

Energy Technology Data Exchange (ETDEWEB)

We study the observational viability of coupled quintessence models with their expansion and growth histories matched to modified gravity cosmologies. We find that for a Dvali-Gabadadze-Porrati model which has been fitted to observations, the matched interacting dark energy models are observationally disfavoured. We also study the distinguishability of interacting dark energy models matched to scalar-tensor theory cosmologies and show that it is not always possible to find a physical interacting dark energy model which shares their expansion and growth histories.

Clemson, Timothy; Koyama, Kazuya, E-mail: timothy.clemson@port.ac.uk, E-mail: kazuya.koyama@port.ac.uk [Institute of Cosmology and Gravitation, University of Portsmouth, Burnaby Road, Portsmouth, PO1 3FX (United Kingdom)

2013-01-01

317

Global features of proton-neutron interactions and symmetry energy  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We study global features of proton-neutron (p-n) interactions and symmetry energy over a wide range of nuclei, using a schematic model interaction with four forces proposed recently. Calculations are performed by the BCS approximation in N,Z=20-50 and N,Z=50-82 regions. The experimental double differences of binding energies and symmetry energy are reproduced quite well. It is shown that the isoscalar p-n interactions with all J are indispensable for explaining the bind...

Kaneko, K.; Hasegawa, M.

1999-01-01

318

Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide-noble-gas interactions  

Science.gov (United States)

We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H2O2-Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry of the H2O2 molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H2O2 molecule, or other systems involving O-O and S-S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O-H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.

Roncaratti, L. F.; Leal, L. A.; Pirani, F.; Aquilanti, V.; e Silva, G. M.; Gargano, R.

2014-10-01

319

Chirality of weakly bound complexes: the potential energy surfaces for the hydrogen-peroxide-noble-gas interactions.  

Science.gov (United States)

We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H2O2-Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry of the H2O2 molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H2O2 molecule, or other systems involving O-O and S-S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O-H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions. PMID:25296808

Roncaratti, L F; Leal, L A; Pirani, F; Aquilanti, V; e Silva, G M; Gargano, R

2014-10-01

320

Low-energy pion-nucleon interaction  

International Nuclear Information System (INIS)

The situation in low-energy pion-nucleon scattering is reviewed, using an energy-dependent PWA as a tool. The method and some conclusions of this new PWA of ?N scattering data across the ?(1232) are summarized. In particular, the ''inconsistencies'' in the low-energy database are addressed, and the state-of-the-art of the NN? coupling constant and of the ?N ?-term is discussed. (orig.)

 
 
 
 
321

Fluctuation-induced interactions in nematics with disordered anchoring energy  

Science.gov (United States)

We examine fluctuation-induced (pseudo-Casimir) interactions in nematic liquid-crystalline films confined between two surfaces, where one of the surfaces imposes a strong homeotropic anchoring (ensuring a uniform mean director profile), while the other one is assumed to be a chemically disordered substrate exhibiting an annealed distribution of anchoring energies. We employ a saddle-point approximation to evaluate the free energy of interaction mediated between the two surfaces and investigate how the interaction force is influenced by the presence of disordered surface anchoring energy. It is shown that the disorder results in a renormalization of the effective surface anchoring parameter in a way that it leads to quantitative and qualitative changes (including a change of sign at intermediate inter-surface separations) in the pseudo-Casimir interaction force when compared with the interaction force in the absence of disorder.

Karimi Pour Haddadan, Fahimeh; Naji, Ali; Shirzadiani, Nafiseh; Podgornik, Rudolf

2014-12-01

322

Interactions of ultrahigh-energy neutrinos  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Future detection of ultrahigh-energy neutrinos will open a new window on physics at center-of-mass energy 10^5 GeV and higher. In particular, observations of neutrino-initiated showers will help test the Standard Model predictions for the neutrino-nucleon cross section.

Kusenko, Alexander

2002-01-01

323

Interacting holographic dark energy models: a general approach  

Science.gov (United States)

Dark energy models inspired by the cosmological holographic principle are studied in homogeneous isotropic spacetime with a general choice for the dark energy density . Special choices of the parameters enable us to obtain three different holographic models, including the holographic Ricci dark energy (RDE) model. Effect of interaction between dark matter and dark energy on the dynamics of those models are investigated for different popular forms of interaction. It is found that crossing of phantom divide can be avoided in RDE models for ?>0.5 irrespective of the presence of interaction. A choice of ?=1 and ?=2/3 leads to a varying ?-like model introducing an IR cutoff length ? -1/2. It is concluded that among the popular choices an interaction of the form Q? H? m suits the best in avoiding the coincidence problem in this model.

Som, S.; Sil, A.

2014-08-01

324

Evolution of Interacting Viscous Dark Energy Model in Einstein Cosmology  

International Nuclear Information System (INIS)

We investigate the evolution of the viscous dark energy (DE) interacting with the dark matter (DM) in the Einstein cosmology model. By using the linearizing theory of the dynamical system, we find that, in our model, there exists a stable late time scaling solution which corresponds to the accelerating universe. We also find the unstable solution under some appropriate parameters. In order to alleviate the coincidence problem, some authors considered the effect of quantum correction due to the conform anomaly and the interacting dark energy with the dark matter. However, if we take into account the bulk viscosity of the cosmic fluid, the coincidence problem will be softened just like the interacting dark energy cosmology model. That is to say, both the non-perfect fluid model and the interacting the dark energy cosmic model can alleviate or soften the singularity of the universe. (geophysics, astronomy, and astrophysics)

325

Hadron-nucleus interactions at high energy  

International Nuclear Information System (INIS)

Properties of energetic secondaries produced at large angles using 800 GeV incident protons are presented. H2, Be, C, Al, Cu and Pb targets were used for the study. The yields for producing such secondaries vary as A/sup ?/ where A is the atomic mass number of the target and ? attains values as large as 1.6. There is evidence that jet-like events have ? values approaching unity, indicating a hard scattering mechanism may be occurring. Events with large values of target-fragmentation energy have, on average, large values of energy in the central region and small values of forward-going energy. Energy flows and number of secondaries are independent of the target when events with similar amounts of energy in the central region are studied

326

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

Science.gov (United States)

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

Fujisawa, Tomotsumi; Nishikawa, Keiko; Shirota, Hideaki

2009-12-01

327

Interacting Ghost Dark Energy in Brans-Dicke Theory  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We investigate the QCD ghost model of dark energy in the framework of Brans-Dicke cosmology. First, we study the non-interacting ghost dark energy in a flat Brans-Dicke theory. In this case we obtain the EoS and the deceleration parameters and a differential equation governing the evolution of ghost energy density. Interestingly enough, we find that the EoS parameter of the non-interacting ghost dark energy can cross the phantom line ($w_D=-1$) provided the parameters of the...

Ebrahimi, Esmaeil; Sheykhi, Ahmad

2011-01-01

328

Interacting holographic dark energy models: A general approach  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Dark energy models inspired by the cosmological holographic principle are studied in homogeneous isotropic spacetime with a general choice for the dark energy density $\\rho_d=3(\\alpha H^2+\\beta\\dot{H})$. Special choices of the parameters enable us to obtain three different holographic models, including the holographic Ricci dark energy(RDE) model. Effect of interaction between dark matter and dark energy on the dynamics of those models are investigated for different popular ...

Som, S.; Sil, A.

2014-01-01

329

High energy e+e- interactions  

International Nuclear Information System (INIS)

A review is given about the experimental studies of e+e- interactions. After a description of the PETRA and PEP storage rings the structure of leptons and the weak neutral current contributions to lepton pair production are discussed. Then experiments for the search for new particles, the jet formation in e+e- annihilation, and the quark and gluon fragmentation are described. (HSI)

330

Interacting Ghost Dark Energy Models in the Higher Dimensional Cosmology  

CERN Document Server

We investigate interacting ghost dark energy models in higher dimensional cosmology. We attempt to model dark matter within a barotropic fluid with $P_{b}=\\omega(t)_{b}\\rho$. In this work we consider four different models based on choosing equation of state parameter and interaction term. We confirm that our models agree with observational data.

Sadeghi, J; Movsisyan, A; Farahani, H

2014-01-01

331

?-? interaction energy in sub(??)6He and OBE potentials  

International Nuclear Information System (INIS)

In this paper we evaluate the ?-? interaction energy in sub(??)6He by using OBE ?-? potentials constructed on the basis of the Nijmegen models. The structure of sub(??)6He was reinvestigated by solving the ? + ? + ? three-body equation, although simple effective interactions were used. (orig./HSI)

332

Impact parameters of inelastic hadron interaction at high energies  

International Nuclear Information System (INIS)

The expression for impact parameters of inelastic hadron-hadron interaction with the defined number of charged particles in the final state is obtained from the absorptive model. The model satisfy the unitary condition in the direct reaction channel. The impact parameters of the inelastic pp interaction at ISR energies are calculated. It is found that the impact parameters of multiple production processes decrease with multiplicity growth and at fixed multiplicity they increase with energy

333

Vibrational Spectra of ??-Type BEDT-TTF Salts: Relationship between Conducting Property, Time-Averaged Site Charge and Inter-Molecular Distance  

Directory of Open Access Journals (Sweden)

Full Text Available The relationship between the conducting behavior and the degree of charge fluctuation in the ??-type BEDT-TTF salts is reviewed from the standpoints of vibrational spectroscopy and crystal structure. A group of ??-type ET salts demonstrates the best model compounds for achieving the above relationship because the two-dimensional structure is simple and great diversity in conducting behavior is realized under ambient pressure. After describing the requirement for the model compound, the methodology for analyzing the results of the vibrational spectra is presented. Vibrational spectroscopy provides the time-averaged molecular charge, the charge distribution in the two-dimensional layer, and the inter-molecular interactions, etc. The experimental results applied to 2/3-filled and 3/4-filled ??-type ET salts are reported. These experimental results suggest that the conducting property, the difference in the time-averaged molecular charges between the ionic and neutral-like sites, the alternation in the inter-molecular distances and the energy levels in the charge distributions are relevant to one another. The difference in the time-averaged molecular charges, ??, is a useful criterion for indicating conducting behavior. All superconductors presented in this review are characterized as small but finite ??.

Takashi Yamamoto

2012-07-01

334

Experimentally based contact energies decode interactions responsible for protein–DNA affinity and the role of molecular waters at the binding interface  

Science.gov (United States)

A major obstacle towards understanding the molecular basis of transcriptional regulation is the lack of a recognition code for protein–DNA interactions. Using high-quality crystal structures and binding data on the promiscuous family of C2H2 zinc fingers (ZF), we decode 10 fundamental specific interactions responsible for protein–DNA recognition. The interactions include five hydrogen bond types, three atomic desolvation penalties, a favorable non-polar energy, and a novel water accessibility factor. We apply this code to three large datasets containing a total of 89 C2H2 transcription factor (TF) mutants on the three ZFs of EGR. Guided by molecular dynamics simulations of individual ZFs, we map the interactions into homology models that embody all feasible intra- and intermolecular bonds, selecting for each sequence the structure with the lowest free energy. These interactions reproduce the change in affinity of 35 mutants of finger I (R2 = 0.998), 23 mutants of finger II (R2 = 0.96) and 31 finger III human domains (R2 = 0.94). Our findings reveal recognition rules that depend on DNA sequence/structure, molecular water at the interface and induced fit of the C2H2 TFs. Collectively, our method provides the first robust framework to decode the molecular basis of TFs binding to DNA. PMID:19429892

Temiz, N. Alpay; Camacho, Carlos J.

2009-01-01

335

Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.  

Science.gov (United States)

A major obstacle towards understanding the molecular basis of transcriptional regulation is the lack of a recognition code for protein-DNA interactions. Using high-quality crystal structures and binding data on the promiscuous family of C(2)H(2) zinc fingers (ZF), we decode 10 fundamental specific interactions responsible for protein-DNA recognition. The interactions include five hydrogen bond types, three atomic desolvation penalties, a favorable non-polar energy, and a novel water accessibility factor. We apply this code to three large datasets containing a total of 89 C(2)H(2) transcription factor (TF) mutants on the three ZFs of EGR. Guided by molecular dynamics simulations of individual ZFs, we map the interactions into homology models that embody all feasible intra- and intermolecular bonds, selecting for each sequence the structure with the lowest free energy. These interactions reproduce the change in affinity of 35 mutants of finger I (R(2) = 0.998), 23 mutants of finger II (R(2) = 0.96) and 31 finger III human domains (R(2) = 0.94). Our findings reveal recognition rules that depend on DNA sequence/structure, molecular water at the interface and induced fit of the C(2)H(2) TFs. Collectively, our method provides the first robust framework to decode the molecular basis of TFs binding to DNA. PMID:19429892

Temiz, N Alpay; Camacho, Carlos J

2009-07-01

336

INTERACTION ENERGIES IN NON WATSON-CRICK PAIRS: AN AB INITIO STUDY OF G·U AND U·U PAIRS  

Directory of Open Access Journals (Sweden)

Full Text Available Ab initio calculations at the MP2/6-31G** level have been carried out on the non-Watson-Crick nucleic acids pairs G·U and U·U to obtain the interaction energies and to see whether the derived values are comparable or not with the canonical G-C, A-T and A-U pairs. Optimized geometries of the pairs show that the structural parameters of the isolated bases differ very little on pairing. The guanine -NH2 group does not participate in the hydrogen bonding formation and possesses a pyramidal structure; its intrinsic nonplanarity plays an important role in the out-of-plane intermolecular interactions. Thus, the G·U pair projects three hydrogen bonding acceptor sites, namely, N7(G, O6(G and O4(U to the RNA major groove. The interaction energy (DHºint calculated for the G·U pair (-13.6 kcal/mol is comparable to that determined for A-T (-13.0 kcal/mol, but considerable smaller than the experimental value reported for G-C (-21.0 kcal/mol. The U·U pair follows the trend that pairing between pyrimidines bases should have lower interacting energies than purine-pyrimidine pairs

SANDRA T MADARIAGA

2005-03-01

337

Interacting ghost dark energy in Brans-Dicke theory  

International Nuclear Information System (INIS)

We investigate the QCD ghost model of dark energy in the framework of Brans-Dicke cosmology. First, we study the non-interacting ghost dark energy in a flat Brans-Dicke theory. In this case we obtain the equation of state and the deceleration parameters and a differential equation governing the evolution of ghost energy density. Interestingly enough, we find that the equation of state parameter of the non-interacting ghost dark energy can cross the phantom line (wD=-1) provided the parameters of the model are chosen suitably. Then, we generalize the study to the interacting ghost dark energy in both flat and non-flat Brans-Dicke framework and find out that the transition of wD to phantom regime can be more easily achieved for than when resort to the Einstein field equations is made.

338

Interacting Ghost Dark Energy in Brans-Dicke Theory  

CERN Document Server

We investigate the QCD ghost model of dark energy in the framework of Brans-Dicke cosmology. First, we study the non-interacting ghost dark energy in a flat Brans-Dicke theory. In this case we obtain the EoS and the deceleration parameters and a differential equation governing the evolution of ghost energy density. Interestingly enough, we find that the EoS parameter of the non-interacting ghost dark energy can cross the phantom line ($w_D=-1$) provided the parameters of the model are chosen suitably. Then, we generalize the study to the interacting ghost dark energy in both flat and non-flat Brans-Dicke framework and find out that the transition of $w_D$ to phantom regime can be more easily achieved for than when resort to the Einstein field equations is made.

Ebrahimi, Esmaeil

2011-01-01

339

Interacting ghost dark energy in Brans-Dicke theory  

Energy Technology Data Exchange (ETDEWEB)

We investigate the QCD ghost model of dark energy in the framework of Brans-Dicke cosmology. First, we study the non-interacting ghost dark energy in a flat Brans-Dicke theory. In this case we obtain the equation of state and the deceleration parameters and a differential equation governing the evolution of ghost energy density. Interestingly enough, we find that the equation of state parameter of the non-interacting ghost dark energy can cross the phantom line (w{sub D}=-1) provided the parameters of the model are chosen suitably. Then, we generalize the study to the interacting ghost dark energy in both flat and non-flat Brans-Dicke framework and find out that the transition of w{sub D} to phantom regime can be more easily achieved for than when resort to the Einstein field equations is made.

Ebrahimi, Esmaeil, E-mail: eebrahimi@uk.ac.ir [Department of Physics, Shahid Bahonar University, PO Box 76175, Kerman (Iran, Islamic Republic of); Research Institute for Astronomy and Astrophysics of Maragha (RIAAM), P. O. Box 55134-441, Maragha (Iran, Islamic Republic of); Sheykhi, Ahmad, E-mail: sheykhi@uk.ac.ir [Department of Physics, Shahid Bahonar University, PO Box 76175, Kerman (Iran, Islamic Republic of); Research Institute for Astronomy and Astrophysics of Maragha (RIAAM), P. O. Box 55134-441, Maragha (Iran, Islamic Republic of)

2011-11-30

340

Anomalous scaling of strong interactions at low energies  

International Nuclear Information System (INIS)

The discovery of scaling in the high energy scattering of hadrons was a crucial step in understanding strong interactions. Hadrons behave at high energies as if they are composed of point like, almost free constituents. The explanation of this phenomenon based on the asymptotic freedom of Yang-Mills theories is one of the triumphs of quantum field theory. The low energy behaviour of strong interactions is far less understood theoretically and there is no systematic way to obtain the low energy scattering amplitudes from QCD because there are no reliable non-perturbative methods in four dimensional quantum field theory. Strong interactions at low energies are described by an approximate theory, the nonlinear sigma model. 12 refs

 
 
 
 
341

Cosmological equation of state and interacting energies  

International Nuclear Information System (INIS)

In this paper we study a model of cosmic evolution, assuming that the different components of the universe could interact between them any time. An effective equation of state (EOS) for the universe has been used as well. A particular function for w, which gives a good agreement between our results and the experimental data, has been studied. Finally, the model obtained has been applied to different important cases

342

Phase-space analysis on interactions in dark energy models  

International Nuclear Information System (INIS)

To alleviate the ''cosmic triple coincidence'' problem, we add two kinds of interacting term in scalar field models which make radiation, matter and dark energy causally connected. Specifically, the interacting term (??2) is being used in dark energy models for the first time. By the phase-space analysis, the evolution of our universe is investigated. We find that the eigenvalues in the radiation dominated phases could be all positive and the interactions help alleviate the ''cosmic triple coincidence'' problem in quintessence model. (orig.)

343

Optimization of intermolecular potential parameters for the CO2/H2O mixture.  

Science.gov (United States)

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

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

2014-10-01

344

Calculations of Potential Energy Surfaces Using Monte Carlo Configuration Interaction  

CERN Document Server

We apply the method of Monte Carlo configuration interaction (MCCI) to calculate ground-state potential energy curves for a range of small molecules and compare the results with full configuration interaction. We show that the MCCI potential energy curve can be calculated to relatively good accuracy, as quantified using the non-parallelity error, using only a very small fraction of the FCI space. In most cases the potential curve is of better accuracy than its constituent single-point energies. We finally test the MCCI program on systems with basis sets beyond full configuration interaction: a lattice of fifty hydrogen atoms and ethylene. The results for ethylene agree fairly well with other computational work while for the lattice of fifty hydrogens we find that the fraction of the full configuration interaction space we were able to consider appears to be too small as, although some qualitative features are reproduced, the potential curve is less accurate.

Coe, J P; Paterson, M J; 10.1063/1.4767052

2012-01-01

345

Dynamics of interacting phantom and quintessence dark energies  

CERN Document Server

We present models, in which phantom energy interacts with two different types of dark energies including variable modified Chaplygin gas (VMCG) and new modified Chaplygin gas (NMCG). We then construct potentials for these cases. It has been shown that the potential of the phantom field decreases from a higher value with the evolution of the Universe.

Farooq, M Umar; Debnath, Ujjal

2011-01-01

346

The ground state energy of an interacting bose gas  

International Nuclear Information System (INIS)

The purpose of this article is to describe some progress in understanding the ground state energy of an interacting Bose gas. In particular we would like to understand if a formula obtained by Bogoliubov does in fact give the correct value for the ground state energy. The validity of the Bogoliubov approximation is examined for a finite and the infinite box. (G.Q.)

347

Probing the relationships between molecular conformation and intermolecular contacts in N,N-dibenzyl-N'-(furan-2-carbonyl)thiourea.  

Science.gov (United States)

In the crystal structure of the title compound, C(20)H(18)N(2)O(2)S, molecules are linked by bifurcated C-H···O hydrogen-bond interactions, giving rise to chains whose links are composed of alternating centrosymmetrically disposed pairs of molecules and characterized by R(2)(2)(10) and R(2)(2)(20) hydrogen-bonding motifs. Also, N-H···S hydrogen bonds form infinite zigzag chains along the [010] direction, which exhibit the C(4) motif. Hirshfeld surface and fingerprint plots were used to explore the intermolecular interactions in the crystal structure. This analysis confirms the important role of C-H···O hydrogen bonds in the molecular conformation and in the crystal structure, providing a potentially useful tool for a full understanding of the intermolecular interactions in acylthiourea derivatives. PMID:22223282

Pérez, Hiram; Corrêa, Rodrigo S; Plutín, Ana María; O'Reilly, Beatriz; Andrade, Marcelo B

2012-01-01

348

Intermediate-energy hadron interactions, II  

Energy Technology Data Exchange (ETDEWEB)

The topics to be covered are as follows. I'll begin with new developments in NN ..-->.. NN..pi.. reactions. This will provide a natural lead-in to the main topic of this talk, which is dibaryons. This will be followed by discussion of elastic proton-deuteron and inelastic proton-alpha scattering. Then there will be a brief mention of two technical developments. Finally, I'll close by giving short remarks about two peculiarities that were found by theorists looking at strong interaction amplitudes. 15 refs., 3 figs.

Silbar, R.R.

1988-01-01

349

Intermediate-energy hadron interactions, II  

International Nuclear Information System (INIS)

The topics to be covered are as follows. I'll begin with new developments in NN ? NN? reactions. This will provide a natural lead-in to the main topic of this talk, which is dibaryons. This will be followed by discussion of elastic proton-deuteron and inelastic proton-alpha scattering. Then there will be a brief mention of two technical developments. Finally, I'll close by giving short remarks about two peculiarities that were found by theorists looking at strong interaction amplitudes. 15 refs., 3 figs

350

Strong interactions studies with medium energy probes  

International Nuclear Information System (INIS)

This report discusses work on: charmonium spectroscopy; proton form- factor in the time-like region; proton-antiproton forward scattering; QCD scaling laws; light quark spectroscopy; high resolutions electron scattering; quasi-free electron scattering; and low energy pion double charge exchange

351

Binding energies of ? ? hypernuclei and the ? ? interaction  

International Nuclear Information System (INIS)

The binding energies of the ? ? hypernuclei /sub ? ?/10Be and /sub ? ?/6He were calculated variationally with a 2? + 2? and with an ? + 2? model respectively. For /sub ? ?/?110Be the integrations were made with Monte Carlo techniques while for /sub ? ?/6He direct numerical methods were used. A wide range of phenomenological ? ? potentials based on meson-exchange models was considered

352

Nucleon-nucleon interaction at medium energies  

International Nuclear Information System (INIS)

A summary of the medium energy nucleon-nucleon elastic and inelastic scattering data is presented from an experimenter's viewpoint. Motivation for additional measurements is given. Experiments which rely on the unique capabilities of the Indiana Cooler are emphasized. 65 references

353

Intermolecular Casimir-Polder Forces in Water and near Surfaces  

CERN Document Server

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

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

2014-01-01

354

Interacting generalized ghost dark energy in non-flat universe  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We investigate the generalized Quantum Chromodynamics (QCD) ghost model of dark energy in the framework of Einstein gravity. First, we study the non-interacting generalized ghost dark energy in a flat Friedmann-Robertson-Walker (FRW) background. We obtain the equation of state parameter, $w_D=p/\\rho$, the deceleration parameter, and the evolution equation of the generalized ghost dark energy. We find that, in this case, $w_D$ cannot cross the phantom line ($w_D>-1$) and even...

Ebrahimi, Esmaeil; Sheykhi, Ahmad; Alavirad, Hamzeh

2012-01-01

355

Binding energy of $\\Lambda$ hypernuclei from realistic YN interactions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

s- and p-wave $\\Lambda$ single-particle enrgies are obtained for a variety of $\\Lambda$ hypernuclei from the relevant self-energy constructed within the framework of a perturbative many-body approach. Results are presented for present realistic hyperon-nucleon interactions such as J\\"{u}lich B and Nijmegen SC models. Effects of the non-locality and energy-dependence of the self-energy on the bound states are investigated.

Vidan?a, I.; Polls, A.; Ramos, A.; Hjorth-jensen, M.

1998-01-01

356

Interacting dark energy and the cosmic coincidence problem  

International Nuclear Information System (INIS)

The introduction of an interaction for dark energy to the standard cosmology offers a potential solution to the cosmic coincidence problem. We examine the conditions on the dark energy density that must be satisfied for this scenario to be realized. Under some general conditions we find a stable attractor for the evolution of the Universe in the future. Holographic conjectures for the dark energy offer some specific examples of models with the desired properties

357

Coherent Rayleigh-Brillouin scattering: Influence of the intermolecular potential  

Science.gov (United States)

The spectrum of the coherent Rayleigh-Brillouin scattering (CRBS) of light by rarefied gas is obtained by solving the Boltzmann equation numerically using the fast spectral method. The influence of the intermolecular potential on the CRBS spectrum is investigated and the accuracy of the prevailing Tenti's s6 kinetic model is evaluated. Our numerical results show that i) the intermolecular potential has a great influence on CRBS spectrum when the Knudsen number is between 0.05 and 1 and ii) the Tenti's s6 kinetic model can only predict the line shape accurately for Maxwell gases at small Knudsen numbers.

Wu, Lei; White, Craig; Scanlon, Thomas J.; Reese, Jason M.; Zhang, Yonghao

2014-12-01

358

Interacting dark sector with variable vacuum energy  

CERN Document Server

We examine a cosmological scenario where dark matter is coupled to a variable vacuum energy while baryons and photons are two decoupled components for a spatially flat Friedmann-Robertson-Walker spacetime. We apply the $\\chi^{2}$ method to the updated observational Hubble data for constraining the cosmological parameters and analyze the amount of dark energy in the radiation era. We show that our model fulfills the severe bound of $\\Omega_{x}(z\\simeq 1100)<0.009$ at the $2\\sigma$ level, so it is consistent with the recent analysis that includes cosmic microwave background anisotropy measurements from the Planck survey, the Atacama Cosmology Telescope, and the South Pole Telescope along with the future constraints achievable by the Euclid and CMBPol experiments, and fulfills the stringent bound $\\Omega_{x}(z\\simeq 10^{10})<0.04$ at the $2\\sigma$ level in the big-bang nucleosynthesis epoch.

Chimento, Luis P; García, Iván E Sánchez

2013-01-01

359

Low-energy antiproton-neon interaction  

International Nuclear Information System (INIS)

By means of a streamer chamber exposed to the LEAR antiproton beams, the total reaction cross sections, the charged-prong multiplicity distributions and lower limits for the production of negative pions and Ksub(s)0 in the anti p-Ne interaction were measured at 19.6, 48.7 and 179.6 MeV. Annihilation was found to be dominant over all other non-elastic anti p-Ne processes. An analysis of Ne and other nuclei data in the frame of the Glauber theory allowed us to determine the ratio between the anti p-n and the anti p-p cross sections. An analysis in the light of INC model predictions allowed us to show up events which can be interpreted as annihilations having occurred deeply inside the nuclei. (orig.)

360

Meson-nuclear interactions at medium energies  

Energy Technology Data Exchange (ETDEWEB)

A brief review of selected directions in medium energy physics is given. Special attention is paid to the propagation of hadrons in the nuclear medium which results in a modification of the free properties of the probe hadron and the nucleus. Such modifications are germane to our understanding of both particles and nuclei. Examples are given involving pion and kaon scattering, absorption and production from nuclei. Some of what has been learned is summarized and some of the hopes for the future are outlined.

Eisenstein, R A

1981-01-01

 
 
 
 
361

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

Science.gov (United States)

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

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

2014-12-01

362

Intermolecular proton transfer in anionic complexes of uracil with alcohols  

International Nuclear Information System (INIS)

A series of eighteen alcohols (ROH) has been designed with an enthalpy of deprotonation (HDP) 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 vertcterized 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

363

Modeling dark energy through an Ising fluid with network interactions  

CERN Document Server

We show that the dark energy effects can be modeled by using an \\emph{Ising perfect fluid} with network interactions, whose low redshift equation of state, i.e. $\\omega_0$, becomes $\\omega_0=-1$ as in the $\\Lambda$CDM model. In our picture, dark energy is characterized by a barotropic fluid on a lattice in the equilibrium configuration. Thus, mimicking the spin interaction by replacing the spin variable with an occupational number, the pressure naturally becomes negative. We find that the corresponding equation of state mimics the effects of a variable dark energy term, whose limiting case reduces to the cosmological constant $\\Lambda$. This permits us to avoid the introduction of a vacuum energy as dark energy source by hand, alleviating the coincidence and fine tuning problems. We find fairly good cosmological constraints, by performing three tests with supernovae Ia, baryonic acoustic oscillation and cosmic microwave background measurements. Finally, we perform the AIC and BIC selection criteria, showing t...

Luongo, Orlando

2013-01-01

364

Kaon nucleon interaction at intermediate energies  

International Nuclear Information System (INIS)

The kaon nucleon system in I=0 and I=1 states is studied in terms of a model lagrangian containing Yukawa terms and contact terms which represent effective short range forces in both isospin states. All Feynman diagrams contributions up to the fourth order are computed and the Pade approximants method to construct S matrix elements satisfying unitarity is used. Using values already determined for the Yukawa coupling constants g(sub)N?K and g(sub)N?K and the well-known value for the scattering length in I=1, it remains as the only free parameter in the model the strength of the contact term in I=0. Results are discussed and compared with available experimental data at low and intermediate energies, for K0p ? K+n, K+p ? K+p and K+d ? K0pp processes. (Author)

365

Low Energy Positron Interactions with Biological Molecules  

Science.gov (United States)

There is some experimental evidence that positrons can produce distinctive molecular fragmentation patterns. It is known that tuning the incident positron energy to near resonance with molecule vibrations can strongly enhance the positron annihilation probability for a molecule. This suggests that fragmentation induced by slow positrons may provide valuable complementary information to existing techniques for identification and study of proteins. In order to study this concept, we are developing a general quantum method for reliably calculating the density distribution for positrons bound to large biological molecules using NEO/GAMESS. We find that the outer molecular orbitals as well as the higher p orbitals on the O atoms contribute heavily to the total annihilation rate. Using the basis sets and approximations we have tested to predict where annihilation occurs can ultimately help us understand the resulting fragmentation patterns of larger biological molecules.

Wanniarachchi, Indika; Morgan, Caroline; Schlegel, Bernhard; Kedziora, Gary; Burgrraf, Larry; Pak, Michael; Hammes-Schiffer, Sharon

2012-10-01

366

Kaon nucleon interaction at intermediate energies  

International Nuclear Information System (INIS)

The kaon nucleon system in I = 0 and I = 1 states is studied in terms of a model lagrangian containing Yukawa terms and contact terms which represent effective short range forces in both isospin states. We compute all Feynman diagrams contributions up to the fourth order and use the Pade approximants method to construct S matrix elements satisfying unitarity. Using values already determined for the Yukawa coupling constants g sub(N?K) and g sub(N?K) and the well-known value for the scattering length in I = 1, it remains as the only free parameter in the model the strength of the contact term in I = 0. Results are discussed and compared with available experimental data at low and intermediate energies, for K0P ? K+n, K+p ? K+p and K+d ? K0pp processes. (Author)

367

Scaling attractors in interacting teleparallel dark energy  

Energy Technology Data Exchange (ETDEWEB)

It has been proposed recently the existence of a non-minimal coupling between a canonical scalar field (quintessence) and gravity in the framework of teleparallel gravity, motivated by similar constructions in the context of General Relativity. The dynamics of the model, known as teleparallel dark energy, has been further developed, but no scaling attractor has been found. Here we consider a model in which the non-minimal coupling is ruled by a dynamically changing coefficient ??f{sub ,?}/(f){sup 1/2}, with f(?) an arbitrary function of the scalar field ?. It is shown that in this case the existence of scaling attractors is possible, which means that the universe will eventually enter these scaling attractors, regardless of the initial conditions. As a consequence, the cosmological coincidence problem could be alleviated without fine-tunings.

Otalora, G., E-mail: giovanni@ift.unesp.br [Instituto de Física Teórica, UNESP-Univ Estadual Paulista Caixa Postal 70532-2, 01156-970 São Paulo (Brazil)

2013-07-01

368

Scaling attractors in interacting teleparallel dark energy  

International Nuclear Information System (INIS)

It has been proposed recently the existence of a non-minimal coupling between a canonical scalar field (quintessence) and gravity in the framework of teleparallel gravity, motivated by similar constructions in the context of General Relativity. The dynamics of the model, known as teleparallel dark energy, has been further developed, but no scaling attractor has been found. Here we consider a model in which the non-minimal coupling is ruled by a dynamically changing coefficient ??f,?/(f)1/2, with f(?) an arbitrary function of the scalar field ?. It is shown that in this case the existence of scaling attractors is possible, which means that the universe will eventually enter these scaling attractors, regardless of the initial conditions. As a consequence, the cosmological coincidence problem could be alleviated without fine-tunings

369

Mutually interacting Tachyon dark energy with variable $G$ and $\\Lambda$  

CERN Document Server

In this paper we consider Tachyonic scalar field as dark energy with interaction between components in the case of variable $G$ and $\\Lambda$. We assume a flat Universe with specific form of scale factor and study cosmological parameters numerically and graphically. Statefinder analysis also performed as well. In the special choice of interaction parameters we succeed to obtain analytical expression of densities. We find that our model will be stable in the late stage but there is an instability at the early Universe.

Hakobyan, J Sadeghi M Khurshudyan M

2013-01-01

370

Post-$Planck$ constraints on interacting vacuum energy  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present improved constraints on an interacting vacuum model using updated astronomical observations including the first data release from Planck. We consider a model with one dimensionless parameter, $\\alpha$, describing the interaction between dark matter and vacuum energy (with fixed equation of state $w=-1$). The background dynamics correspond to a generalised Chaplygin gas cosmology, but the perturbations have a zero sound speed. The tension between the value of the H...

Wang, Yuting; Wands, David; Zhao, Gong-bo; Xu, Lixin

2014-01-01

371

On the Casimir Energy of Frequency Dependent Interactions  

CERN Document Server

Vacuum polarization (or Casimir) energies can be straightforwardly computed from scattering data for static field configurations whose interactions with the fluctuating field are frequency independent. In effective theories, however,such interactions are typically frequency dependent. As a consequence, the relationship between scattering data and the Green's function is modified, which may or may not induce additional contributions to the vacuum polarization energy. We discuss several examples that naturally include frequency dependent interactions: (i) scalar electrodynamics with a static background potential, (ii) an effective theory that emerges from integrating out a heavy degree of freedom, and (iii) quantum electrodynamics coupled to a frequency dependent dielectric material. In the latter case, we argue that introducing dissipation as required by the Kramers-Kronig relations requires the consideration of the Casimir energy within a statistical mechanics formalism, while in the absence of dissipation we...

Graham, N; Weigel, H

2014-01-01

372

Calibration of the interaction energy between Bose and Fermi superfluids  

Science.gov (United States)

In this paper we study the interaction energy in a mixture of Bose and Fermi superfluids realized in recent cold atom experiments. On the Bose-Einstein-condensate (BEC) side of a Feshbach resonance between fermionic atoms, this interaction energy can be directly related to the scattering length between a bosonic atom and a dimer composed of fermions. We calculate the atom-dimer scattering length from a three-body analysis with both a zero-range model and a separable model, including the van der Waals length scale, and we find significant deviation from the result given by a mean-field approach. We also find that the multiple scattering between atom and dimer can account for such a deviation. Our results provide a calibration to the mean-field interaction energy, which can be verified by measuring the shift of collective oscillation frequency.

Zhang, Ren; Zhang, Wei; Zhai, Hui; Zhang, Peng

2014-12-01

373

Photochemistry on surfaces. Intermolecular energy electron transfer processes between excited Ru(bpy){sub 3}{sup 2+} and H-aggregates of cresyl violet on SiO{sub 2} and SnO{sub 2} colloids  

Energy Technology Data Exchange (ETDEWEB)

Cresyl violet, a cationic dye (CV{sup +}), forms H-aggregates on the negatively charged SiO{sub 2} and SnO{sub 2} colloids. These aggregates exhibit broad absorbance around 520 nm. By coadsorbing a sensitizer, Ru(bpy){sub 3}{sup 2+}, we are able to characterize the triplet excited state and reduced form of dye-aggregates on the colloidal SiO{sub 2} and SnO{sub 2} suspensions. On SiO{sub 2} surfaces, the excited state quenching of Ru(bpy){sub 3}{sup 2+} by dye-aggregates proceeds via an energy transfer mechanism. Picosecond laser flash photolysis experiments indicate that such a surface-promoted energy transfer is completed within 20 ps. On the other hand dye-aggregates adsorbed onto SnO{sub 2} colloids undergo photosensitized reduction since the excited sensitizer, Ru(bpy){sub 3} {sup 2+}, is efficiently quenched by the semiconductor support. The role of support material in promoting energy and electron transfer processes is described. 87 refs., 11 figs.

Liu, D.; Hug, G.L.; Kamat, P.V. [Univ. of Notre Dame, IN (United States)

1995-11-09

374

Simulated Galaxy Interactions as Probes of Merger Spectral Energy Distributions  

Science.gov (United States)

We present the first systematic comparison of ultraviolet-millimeter spectral energy distributions (SEDs) of observed and simulated interacting galaxies. Our sample is drawn from the Spitzer Interacting Galaxy Survey and probes a range of galaxy interaction parameters. We use 31 galaxies in 14 systems which have been observed with Herschel, Spitzer, GALEX, and 2MASS. We create a suite of GADGET-3 hydrodynamic simulations of isolated and interacting galaxies with stellar masses comparable to those in our sample of interacting galaxies. Photometry for the simulated systems is then calculated with the SUNRISE radiative transfer code for comparison with the observed systems. For most of the observed systems, one or more of the simulated SEDs match reasonably well. The best matches recover the infrared luminosity and the star formation rate of the observed systems, and the more massive systems preferentially match SEDs from simulations of more massive galaxies. The most morphologically distorted systems in our sample are best matched to the simulated SEDs that are close to coalescence, while less evolved systems match well with the SEDs over a wide range of interaction stages, suggesting that an SED alone is insufficient for identifying the interaction stage except during the most active phases in strongly interacting systems. This result is supported by our finding that the SEDs calculated for simulated systems vary little over the interaction sequence.

Lanz, Lauranne; Hayward, Christopher C.; Zezas, Andreas; Smith, Howard A.; Ashby, Matthew L. N.; Brassington, Nicola; Fazio, Giovanni G.; Hernquist, Lars

2014-04-01

375

Gold-catalyzed intermolecular hydroamination of allenes with sulfonamides  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A co-catalyst of (PPh3)AuCl/AgOTf for the intermolecular hydroamination of allenes with sulfonamides is shown. The reaction proceeded smoothly under mild conditions for differently substituted allenes giving N-allylic sulfonamides in good yields with high regioselectivity and E-selectivity.

Zhang, Chen; Zhang, Shao-qiao; Cai, Hua-jun; Cui, Dong-mei

2013-01-01

376

Gold-catalyzed intermolecular hydroamination of allenes with sulfonamides  

Science.gov (United States)

Summary A co-catalyst of (PPh3)AuCl/AgOTf for the intermolecular hydroamination of allenes with sulfonamides is shown. The reaction proceeded smoothly under mild conditions for differently substituted allenes giving N-allylic sulfonamides in good yields with high regioselectivity and E-selectivity. PMID:23766819

Zhang, Shao-Qiao; Cai, Hua-Jun

2013-01-01

377

Coiodação de alquenos com nucleófilos oxigenados: reações intermoleculares  

Directory of Open Access Journals (Sweden)

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.

Sanseverino Antonio Manzolillo

2001-01-01

378

Strong impact of protonation and deprotonation on intermolecular Coulombic decay  

International Nuclear Information System (INIS)

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

379

Strong impact of protonation and deprotonation on intermolecular Coulombic decay  

Science.gov (United States)

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

Kryzhevoi, Nikolai V.; Cederbaum, Lorenz S.

2012-11-01

380

Simulated Galaxy Interactions as Probes of Merger Spectral Energy Distributions  

CERN Document Server

We present the first systematic comparison of ultraviolet-millimeter spectral energy distributions (SEDs) of observed and simulated interacting galaxies. Our sample is drawn from the Spitzer Interacting Galaxy Survey, and probes a range of galaxy interaction parameters. We use 31 galaxies in 14 systems which have been observed with Herschel, Spitzer, GALEX, and 2MASS. We create a suite of GADGET-3 hydrodynamic simulations of isolated and interacting galaxies with stellar masses comparable to those in our sample of interacting galaxies. Photometry for the simulated systems is then calculated with the SUNRISE radiative transfer code for comparison with the observed systems. For most of the observed systems, one or more of the simulated SEDs match reasonably well. The best matches recover the infrared luminosity and the star formation rate of the observed systems, and the more massive systems preferentially match SEDs from simulations of more massive galaxies. The most morphologically distorted systems in our sa...

Lanz, Lauranne; Zezas, Andreas; Smith, Howard A; Ashby, Matthew L N; Brassington, Nicola; Fazio, Giovanni G; Hernquist, Lars

2014-01-01

 
 
 
 
381

Interactions of Policies for Renewable Energy and Climate  

Energy Technology Data Exchange (ETDEWEB)

This paper explores the relationships between climate policy and renewable energy policy instruments. It shows that, even where CO2 emissions are duly priced, specific incentives for supporting the early deployment of renewable energy technologies are justified by the steep learning curves of nascent technologies. This early investment reduces costs in the longer term and makes renewable energy affordable when it needs to be deployed on a very large scale to fully contribute to climate change mitigation and energy security. The paper also reveals other noteworthy interaction effects of climate policy and renewable policy instruments on the wholesale electricity prices in deregulated markets, which open new areas for future research.

NONE

2011-07-01

382

New particles and interactions at high energy muon colliders  

International Nuclear Information System (INIS)

I give an overview of the ability of a high energy ?+?- collider to discover new particles and interactions. I start with heavy fermions which will be the most straightforward to produce and observe. I then discuss single leptoquark production which is produced via the quark content of the photon and the discovery potential for extra gauge bosons which will inanifest themselves via deviations of observables from their standard model values. Finally, contact interactions are studied as the generalization of looking for new interactions via deviations from the standard model

383

New Particles and Interactions at High Energy Muon Colliders  

CERN Document Server

I give an overview of the ability of a high energy $\\mu^+\\mu^-$ collider to discover new particles and interactions. I start with heavy fermions which will be the most straightforward to produce and observe. I then discuss single leptoquark production which is produced via the quark content of the photon and the discovery potential for extra gauge bosons which will manifest themselves via deviations of observables from their standard model values. Finally, contact interactions are studied as the generalization of looking for new interactions via deviations from the standard model.

Godfrey, S

1998-01-01

384

Transition of the dark energy equation of state in an interacting holographic dark energy model  

International Nuclear Information System (INIS)

A model of holographic dark energy with an interaction with matter fields has been investigated. Choosing the future event horizon as an IR cutoff, we have shown that the ratio of energy densities can vary with time. With the interaction between the two different constituents of the universe, we observed the evolution of the universe, from early deceleration to late time acceleration. In addition, we have found that such an interacting dark energy model can accommodate a transition of the dark energy from a normal state where wD>-1 to wD<-1 phantom regimes. Implications of interacting dark energy model for the observation of dark energy transition has been discussed

385

Thomas precession and spin interaction energy in very special relativity  

Science.gov (United States)

Very Special Relativity (VSR), proposed by Cohen and Glashow, considers one of the subgroups of Poincaré group as the symmetry of spacetime. This paper investigates the transformations of electromagnetic fields under boosts of VSR, and by the aid of them studies the interaction energy between spin of an electron and external electromagnetic fields. Here, we argue that Thomas precession, one of the consequences of Special Relativity (SR), does not exist in HOM(2) avatar of VSR. The predictions of SR and VSR about the spin interaction energy in a certain case are compared, and despite the absence of Thomas precession in VSR, no noticeable departure is seen.

Ganjitabar, Hassan; Shojai, Ali

2014-08-01

386

Thermodynamical picture of the interacting holographic dark energy model  

CERN Document Server

In the present paper, we provide a thermodynamical interpretation for the holographic dark energy model in a non-flat universe. For this case, the characteristic length is no more the radius of the event horizon ($R_E$) but the event horizon radius as measured from the sphere of the horizon ($L$). Furthermore, when interaction between the dark components of the holographic dark energy model in the non-flat universe is present its thermodynamical interpretation changes by a stable thermal fluctuation. A relation between the interaction term of the dark components and this thermal fluctuation is obtained.

Setare, M R

2009-01-01

387

Correlation energies in the random phase approximation using realistic interactions  

CERN Document Server

The self-consistent random phase approximation (RPA) based on a correlated realistic nucleon-nucleon interaction is used to evaluate correlation energies in closed-shell nuclei beyond the Hartree-Fock level. The relevance of contributions associated with charge exchange excitations as well as the necessity to correct for the double counting of the second order contribution to the RPA ring summation are emphasized. Once these effects are properly accounted for, the RPA ring summation provides an efficient tool to assess the impact of long-range correlations on binding energies throughout the whole nuclear chart, which is of particular importance when starting from realistic interactions.

Barbieri, C; Papakonstantinou, P; Roth, R

2006-01-01

388

No strings attached potential vs. interaction energy in QCD  

Energy Technology Data Exchange (ETDEWEB)

In infrared-stable fixed-point field theories, the interaction energy of a test particle is proportional to the non-relativistic (heavy source) coordinate-space potential derived from the field strength produced by that source. This is no longer true in ultraviolet-stable fixed-point field theories (UVSFPFT) as they may not have a finite infrared fixed point. This leads to the possibility that UVSFPFTs may have quite conventional field strength distributions despite the unusual spatial dependence expected for the interaction energy.

Goldman, T.

1996-10-20

389

No strings attached potential vs. interaction energy in QCD  

International Nuclear Information System (INIS)

In infrared-stable fixed-point field theories, the interaction energy of a test particle is proportional to the non-relativistic (heavy source) coordinate-space potential derived from the field strength produced by that source. This is no longer true in ultraviolet-stable fixed-point field theories (UVSFPFT) as they may not have a finite infrared fixed point. This leads to the possibility that UVSFPFTs may have quite conventional field strength distributions despite the unusual spatial dependence expected for the interaction energy

390

Constraints on interacting Dark Energy models from galaxy rotation curves  

International Nuclear Information System (INIS)

Interacting Dark Energy models have been introduced as a possible alternative to the standard ?CDM concordance cosmological scenario in order to ease the fine-tuning problems of the cosmological constant. However, the interaction of the Dark Energy field with other massive particles in the universe induces also an effective modification of structure formation processes, leading to a different dynamical behavior of density perturbations with respect to the standard scenario. In particular, high-resolution N-body simulations have recently shown that also the structural properties of highly nonlinear objects, as e.g. their average concentration at a given mass, could be significantly modified in the presence of an interaction between Dark Energy and Dark Matter. While a constant interaction strength leads to less concentrated density profiles, a steep growth in time of the coupling function has been shown to determine a large increase of halo concentrations over a wide range of masses, including the typical halos hosting luminous spiral galaxies. This determines a substantial worsening of the 'cusp-core' tension arising in the standard ?CDM model and provides a direct way to constrain the form of the Dark Energy interaction. In the present paper we make use of the outcomes of some high-resolution N-body simulations of a specific class of interacting Dark Energy models to compare the predicted rotation curves of luminous spiral galaxies forming in these cosmologies against real observational data. Our results show how some specific interacting Dark Energy scenarios featuring a steep growth in time of the coupling function — which are virtually indistinguishable from ?CDM in the background — cannot fit the observed rotation curves of luminous spiral galaxies and can therefore be ruled out only on the basis of dynamical properties of small-scale structures. Our study is a pilot investigation of the effects of a Dark Energy interaction at small scales, and demonstrates how the dynamical properties of visible galaxies can in some cases provide direct constraints on the nature of Dark Energy

391

Interacting scales and energy transfer in isotropic turbulence  

Science.gov (United States)

The dependence of the energy transfer process on the disparity of the interacting scales is investigated in the inertial and far-dissipation ranges of isotropic turbulence. The strategy for generating the simulated flow fields and the choice of a disparity parameter to characterize the scaling of the interactions is discussed. The inertial range is found to be dominated by relatively local interactions, in agreement with the Kolmogorov assumption. The far-dissipation is found to be dominated by relatively non-local interactions, supporting the classical notion that the far-dissipation range is slaved to the Kolmogorov scales. The measured energy transfer is compared with the classical models of Heisenberg, Obukhov, and the more detailed analysis of Tennekes and Lumley. The energy transfer statistics measured in the numerically simulated flows are found to be nearly self-similar for wave numbers in the inertial range. Using the self-similar form measured within the limited scale range of the simulation, an 'ideal' energy transfer function and the corresponding energy flux rate for an inertial range of infinite extent are constructed. From this flux rate, the Kolmogorov constant is calculated to be 1.5, in excellent agreement with experiments.

Zhou, YE

1993-01-01

392

Intermolecular Hydrogen Transfer in Isobutane Hydrate  

Directory of Open Access Journals (Sweden)

Full Text Available Electron spin resonance (ESR spectra of butyl radicals induced with ?-ray irradiation in the simple isobutane (2-methylpropane hydrate (prepared with deuterated water were investigated. Isothermal annealing results of the ?-ray-irradiated isobutane hydrate reveal that the isobutyl radical in a large cage withdraws a hydrogen atom from the isobutane molecule through shared hexagonal-faces of adjacent large cages. During this “hydrogen picking” process, the isobutyl radical is apparently transformed into a tert-butyl radical, while the sum of isobutyl and tert-butyl radicals remains constant. The apparent transformation from isobutyl to tert-butyl radicals is an irreversible first-order reaction and the activation energy was estimated to be 35 ± 3 kJ/mol, which was in agreement with the activation energy (39 ± 5 kJ/mol of hydrogen picking in the ?-ray-irradiated propane hydrate with deuterated water.

Takeshi Sugahara

2012-05-01

393

Identifying the intermolecular hydrogen-bonding supramolecular synthons in an indomethacin-nicotinamide cocrystal by solid-state NMR.  

Science.gov (United States)

Two-dimensional (1)H double-quantum and (14)N-(1)H & (1)H-(13)C heteronuclear magic-angle spinning (MAS) NMR spectra recorded at natural isotopic abundance identify specific intermolecular COOH···N(arom) and CH(arom)···O=C hydrogen-bonding interactions in the solid-state structure of an indomethacin-nicotinamide cocrystal, thus additionally proving cocrystal formation. PMID:23023334

Maruyoshi, Keisuke; Iuga, Dinu; Antzutkin, Oleg N; Alhalaweh, Amjad; Velaga, Sitaram P; Brown, Steven P

2012-11-14

394

Study of the energy flux during plasma/surface interaction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The knowledge of the energy flux during plasma/surface interactions is a key parameter for the control of low pressure plasmas, as sputter deposition or etching processes. The energy flux density at a surface depends on plasma species (ions, electrons, neutrals...) elementary processes (condensation, chemical reaction, radiative transfer). It can be obtained by carring out simulation of particule transport through the plasma, by the calculation of each energetic contribution from plasma param...

Cormier, Pierre-antoine

2012-01-01

395

Self-interaction errors in nuclear energy density functionals  

Digital Repository Infrastructure Vision for European Research (DRIVER)

When applied to a single nucleon, nuclear energy density functionals may yield a non-vanishing internal energy thus implying that the nucleon is interacting with itself. It is shown how to avoid this unphysical feature for semi-local phenomenological functionals containing all possible bilinear combinations of local densities and currents up to second order in the derivatives. The method outlined in this Rapid Communication could be easily extended to functionals containing ...

Chamel, N.

2010-01-01

396

Distributed energy resources in grid interactive AC microgrids  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Increased penetration of distributed energy resources (DER) and large-scale deployment of renewable energy sources are challenging the entire architecture of traditional power system. Microgrid, featuring higher flexibility and reliability, becomes an attractive candidate for the configuration of future electrical power system. This paper gives an overview of DER units in the grid interactive ac microgrid. The options in structures and control methods of power electronics interfaced DER units...

Wang, Xiongfei; Guerrero, Josep; Chen, Zhe; Blaabjerg, Frede

2010-01-01

397

PCAC and nuclear shadowing of neutrino interaction at high energies  

International Nuclear Information System (INIS)

Consequences of hypothesis of partially conserved axial current (PCAC) at high energies are considered. On the contrary to widely spread opinion space-time patterns of shadowing are quite different in cases of neutrino and photon interactions. The main source of shadowing is rather real process of diffractive neutrino production on nuclear nucleons than spontaneous emission of long-living hadronic fluctuations. This results in saturation of nuclear shadowing at rather low energy. 21 refs.; 9 figs

398

New Evidence for Interacting Dark Energy from BOSS  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this Letter we show that an interaction between dark matter and dark energy is favored by the most recent large scale structure observations. The result presented by the BOSS-SDSS collaboration measuring the baryon acoustic oscillations of the Ly-$\\alpha$ forest from high redshift quasars indicates a $2.5\\sigma$ departure from the standard $\\Lambda$CDM model. This is the first time that the evolution of dark energy at high redshifts has been measured and the current resul...

Abdalla, E.; Ferreira, Elisa G. M.; Quintin, Jerome; Wang, Bin

2014-01-01

399

New holographic dark energy model with non-linear interaction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this paper the cosmological evolution of a holographic dark energy model with a non-linear interaction between the dark energy and dark matter components in a FRW type flat universe is analysed. In this context, the deceleration parameter $q$ and the equation state $w_{\\Lambda}$ are obtained. We found that, as the square of the speed of sound remains positive, the model is stable under perturbations since early times; it also shows that the evolution of the matter and dar...

Oliveros, A.; Acero, Mario A.

2014-01-01

400

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

Science.gov (United States)

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

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

 
 
 
 
401

Hadronic interactions for high energy cosmic ray air showers  

International Nuclear Information System (INIS)

Understanding hadronic interactions at high energies represents a very important ingredient for modeling high energy cosmic ray air showers. In this paper, a new approach to simulate hadronic interactions is presented, including hadron-hadron, hadron-nucleus, and nucleus-nucleus scattering. Such collisions are very complex, being composed of many components, and therefore some strategy is needed to construct a reliable model. The central point of our approach is the hypothesis, that the behavior of high energy interactions is universal (universality hypothesis). A model for hadronic interactions is constructed in a modular fashion. The individual modules, based on the universality hypothesis, are identified as building blocks for more elementary interactions (like e+e-, lepton-proton), and can therefore be studied in a much simpler context. With these building blocks under control, a quite reliable model is proposed for nucleus-nucleus, hadron-nucleus and hadron-hadron scattering, providing in particular very useful tests for the complicated numerical procedures using Monte Carlo techniques. (K.A.)

402

Dark Energy Problem in a Four-Fermion Interaction Model  

CERN Document Server

Cosmology enters precision testing period with the observational experiments advancement. We have not arrived to decipher the origin of the dominant dark energy component of our universe, although we have located some of its characters. In such a situation the possibilities of a simple four-fermion interaction model are investigated to describe dark energy characters. We explicitly calculate the vacuum expectation value of the energy-momentum tensor and discuss the results with comparison to the equation of state for dark energy requirement. It is found that the negative pressure is realized at low temperature. It is an appropriate property as a dark energy candidate. We also investigate some cosmological tests for the dark energy via its equation of state.

Inagaki, T; Murata, T; Murata, Tsukasa

2003-01-01

403

THz absorption spectrum of the CO2-H2O complex: Observation and assignment of intermolecular van der Waals vibrations  

DEFF Research Database (Denmark)

Terahertz absorption spectra have been recorded for the weakly bound CO2-H2O complex embedded in cryogenic neon matrices at 2.8 K. The three high-frequency van der Waals vibrational transitions associated with out-of-plane wagging, in-plane rocking, and torsional motion of the isotopic H2O subunit have been assigned and provide crucial observables for benchmark theoretical descriptions of this systems' flat intermolecular potential energy surface. A (semi)-empirical value for the zero-point energy of 273 ± 15 cm-1 from the class of intermolecular van der Waals vibrations is proposed and the combination with high-level quantum chemical calculations provides a value of 726 ± 15 cm-1 for the dissociation energy D0. © 2014 AIP Publishing LLC.

Andersen, Jonas; Heimdal, J.

2014-01-01

404

THz absorption spectrum of the CO2–H2O complex: Observation and assignment of intermolecular van der Waals vibrations  

DEFF Research Database (Denmark)

Terahertz absorption spectra have been recorded for the weakly bound CO2–H2O complex embedded in cryogenic neon matrices at 2.8 K. The three high-frequency van der Waals vibrational transitions associated with out-of-plane wagging, in-plane rocking, and torsional motion of the isotopic H2O subunit have been assigned and provide crucial observables for benchmark theoretical descriptions of this systems’ flat intermolecular potential energy surface. A (semi)-empirical value for the zero-point energy of 273 ± 15 cm?1 from the class of intermolecular van der Waals vibrations is proposed and the combination with high-level quantum chemical calculations provides a value of 726 ± 15 cm?1 for the dissociation energy D0

Andersen, Jonas; Heimdal, J.

2014-01-01

405

Energy transfer via protein-protein interaction in Renilla bioluminescence  

Energy Technology Data Exchange (ETDEWEB)

Radiationless energy transfer is known to play biologically important roles in both photosynthesis and bioluminescence. In photosynthesis, accessory pigments serve as antennae, transferring excitation energy into the reaction centers. In the bioluminescent coelenterates, energy is transferred from the site of reaction via an accessory protein known as the green-fluorescent protein (GFP). Coelenterate bioluminescence systems such as that of the sea pansy, Renilla, are well characterized biochemically, and their energy transfer process can be duplicated in vitro using isolated and purified components. We have measured efficient in vitro energy transfer from the electronic excited state of the enzyme-bound oxyluciferin to the green-fluorescent protein at protein concentrations of 0.1 ..mu..M. We have also demonstrated a 1:1 complex between these proteins, under conditions of energy transfer, by the chromatographic technique of Hummel and Dreyer. These observations indicate that bioluminescent energy transfer is mediated via protein-protein interaction. Furthermore, with inter-species cross-reaction studies and protein modification techniques we have shown that the interaction between luciferase and GFP is highly specific. These features make the Renilla system an attractive alternative to the photosynthetic systems as a tool for studying radiationless energy transfer.

Ward, W.W.; Cormier, M.J.

1978-01-01

406

Experimental studies of pion-nucleus interactions at intermediate energies  

International Nuclear Information System (INIS)

This report summarizes the work on experimental research in intermediate energy nuclear physics carried out at New Mexico State University in 1991 under a great from the US Department of Energy. Most of these studies have involved investigations of various pion-nucleus i