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Sample records for intermolecular interaction potential

  1. Intermolecular interactions

    International Nuclear Information System (INIS)

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

    1978-01-01

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

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

    International Nuclear Information System (INIS)

    Chen Xiangrong; Bai Yulin; Zhu Jun; Yang Xiangdong

    2004-01-01

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

  3. Characterizing the Polymer:Fullerene Intermolecular Interactions

    KAUST Repository

    Sweetnam, Sean

    2016-02-02

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

  4. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, Anders S., E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Cui, Qiang, E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu [Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706 (United States); Elstner, Marcus [Theoretische Chemische Biologie, Universität Karlsruhe, Kaiserstr. 12, 76131 Karlsruhe (Germany)

    2015-08-28

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Science.gov (United States)

    2017-01-01

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

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

    Science.gov (United States)

    Lovelock, Kevin R J

    2017-12-01

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

  8. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    Directory of Open Access Journals (Sweden)

    Venkatesha R. Hathwar

    2015-09-01

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

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

    Science.gov (United States)

    Varfolomeeva, Vera V.; Terentev, Alexey V.

    2018-01-01

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

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

    Science.gov (United States)

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

    2012-02-01

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

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

    International Nuclear Information System (INIS)

    Stiegler, Thomas; Sadus, Richard J.

    2015-01-01

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

  12. Characterizing the Polymer:Fullerene Intermolecular Interactions

    KAUST Repository

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

    Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

    1980-01-01

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

  15. Intermolecular interactions in the condensed phase

    DEFF Research Database (Denmark)

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

    2017-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Xantheas, Sotiris S.

    2004-05-01

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

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

    Science.gov (United States)

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

    2018-04-25

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

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

    African Journals Online (AJOL)

    ADOWIE PERE

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

  19. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide.

    Science.gov (United States)

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

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.

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

    Directory of Open Access Journals (Sweden)

    Saied M. Soliman

    2016-12-01

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

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

    Science.gov (United States)

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

    2013-04-08

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

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

    International Nuclear Information System (INIS)

    Askadskii, Andrei A

    1999-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    KAUST Repository

    Sutton, Christopher

    2015-10-30

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

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

    Science.gov (United States)

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

    2010-07-29

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

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

    Directory of Open Access Journals (Sweden)

    Cia-Hin Lau

    2012-01-01

    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.

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

    Science.gov (United States)

    Berry, David J; Steed, Jonathan W

    2017-08-01

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

  10. Study of interaction in silica glass via model potential approach

    Science.gov (United States)

    Mann, Sarita; Rani, Pooja

    2016-05-01

    Silica is one of the most commonly encountered substances in daily life and in electronics industry. Crystalline SiO2 (in several forms: quartz, cristobalite, tridymite) is an important constituent of many minerals and gemstones, both in pure form and mixed with related oxides. Cohesive energy of amorphous SiO2 has been investigated via intermolecular potentials i.e weak Van der Waals interaction and Morse type short-range interaction. We suggest a simple atom-atom based Van der Waals as well as Morse potential to find cohesive energy of glass. It has been found that the study of silica structure using two different model potentials is significantly different. Van der Waals potential is too weak (P.E =0.142eV/molecule) to describe the interaction between silica molecules. Morse potential is a strong potential, earlier given for intramolecular bonding, but if applied for intermolecular bonding, it gives a value of P.E (=-21.92eV/molecule) to appropriately describe the structure of silica.

  11. Controlled Self-Assembly of Low-Dimensional Alq3 Nanostructures from 1D Nanowires to 2D Plates via Intermolecular Interactions

    Science.gov (United States)

    Gu, Jianmin; Yin, Baipeng; Fu, Shaoyan; Jin, Cuihong; Liu, Xin; Bian, Zhenpan; Li, Jianjun; Wang, Lu; Li, Xiaoyu

    2018-03-01

    Due to the intense influence of the shape and size of the photon building blocks on the limitation and guidance of optical waves, an important strategy is the fabrication of different structures. Herein, organic semiconductor tris-(8-hydroxyquinoline)aluminium (Alq3) nanostructures with controllable morphology, ranging from one-dimensional nanowires to two-dimensional plates, have been prepared through altering intermolecular interactions with employing the anti-solvent diffusion cooperate with solvent-volatilization induced self-assembly method. The morphologies of the formed nanostructures, which are closely related to the stacking modes of the molecules, can be exactly controlled by altering the polarity of anti-solvents that can influence various intermolecular interactions. The synthesis strategy reported here can potentially be extended to other functional organic nanomaterials.

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

    Science.gov (United States)

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

    2018-06-01

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

  13. Determination of a silane intermolecular force field potential model from an ab initio calculation

    International Nuclear Information System (INIS)

    Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng

    2010-01-01

    Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.

  14. Modulation of intermolecular interactions in single-molecule magnets

    Science.gov (United States)

    Heroux, Katie Jeanne

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

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

    International Nuclear Information System (INIS)

    Coroiu, Ilioara

    2004-01-01

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

  16. Study of interaction in silica glass via model potential approach

    Energy Technology Data Exchange (ETDEWEB)

    Mann, Sarita, E-mail: saritaiitr2003@gmail.com [Department of Physics, Panjab University, Chandigarh-160014 (India); Rani, Pooja [D.A.V. College, Sec-10, Chandigarh-160010 (India)

    2016-05-06

    Silica is one of the most commonly encountered substances in daily life and in electronics industry. Crystalline SiO{sub 2} (in several forms: quartz, cristobalite, tridymite) is an important constituent of many minerals and gemstones, both in pure form and mixed with related oxides. Cohesive energy of amorphous SiO{sub 2} has been investigated via intermolecular potentials i.e weak Van der Waals interaction and Morse type short-range interaction. We suggest a simple atom-atom based Van der Waals as well as Morse potential to find cohesive energy of glass. It has been found that the study of silica structure using two different model potentials is significantly different. Van der Waals potential is too weak (P.E =0.142eV/molecule) to describe the interaction between silica molecules. Morse potential is a strong potential, earlier given for intramolecular bonding, but if applied for intermolecular bonding, it gives a value of P.E (=−21.92eV/molecule) to appropriately describe the structure of silica.

  17. Testing intermolecular potential functions using transport property data

    International Nuclear Information System (INIS)

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

    1975-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-20

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

  19. Localized-overlap approach to calculations of intermolecular interactions

    Science.gov (United States)

    Rob, Fazle

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

  20. Intermolecular interaction studies of glyphosate with water

    Science.gov (United States)

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

    2017-07-01

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

  1. Calculation of intermolecular potentials for H2−H2 and H2−O2 dimers ab initio and prediction of second virial coefficients

    International Nuclear Information System (INIS)

    Pham Van, Tat; Deiters, Ulrich K.

    2015-01-01

    Highlights: • We construct the angular orientations of dimers H 2 −H 2 and H 2 −O 2 . • We calculate the ab initio intermolecular interaction energies for all built orientations. • Extrapolating the interaction energies to the complete basis set limit aug-cc-pV23Z. • We develop two 5-site ab initio intermolecular potentials of dimers H 2 −H 2 , H 2 −O 2 . • Calculating the virial coefficients of dimer H 2 −H 2 and H 2 −O 2 . - Abstract: The intermolecular interaction potentials of the dimers H 2 −H 2 and H 2 −O 2 were calculated from quantum mechanics, using coupled-cluster theory CCSD(T) and correlation-consistent basis sets aug-cc-pVmZ (m = 2, 3); the results were extrapolated to the basis set limit aug-cc-pV23Z. The interaction energies were corrected for the basis set superposition error with the counterpoise scheme. For comparison also Møller–Plesset perturbation theory (at levels 2–4) with the basis sets aug-cc-pVTZ were considered, but the results proved inferior. The quantum mechanical results were used to construct analytical pair potential functions. From these functions the second virial coefficients of hydrogen and the cross virial coefficients of the hydrogen–oxygen system were obtained by integration; in both cases corrections for quantum effects were included. The results agree well with experimental data, if available, or with empirical correlations

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

    Science.gov (United States)

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

    2014-04-05

    The rate coefficients for N2-N2 collision-induced vibrational energy exchange (important for the enhancement of several modern innovative technologies) have been computed over a wide range of temperature. Potential energy surfaces based on different formulations of the intramolecular and intermolecular components of the interaction have been used to compute quasiclassically and semiclassically some vibrational to vibrational energy transfer rate coefficients. Related outcomes have been rationalized in terms of state-to-state probabilities and cross sections for quasi-resonant transitions and deexcitations from the first excited vibrational level (for which experimental information are available). On this ground, it has been possible to spot critical differences on the vibrational energy exchange mechanisms supported by the different surfaces (mainly by their intermolecular components) in the low collision energy regime, though still effective for temperatures as high as 10,000 K. It was found, in particular, that the most recently proposed intermolecular potential becomes the most effective in promoting vibrational energy exchange near threshold temperatures and has a behavior opposite to the previously proposed one when varying the coupling of vibration with the other degrees of freedom. Copyright © 2014 Wiley Periodicals, Inc.

  3. Resonance energy transfer (RET)-Induced intermolecular pairing force: a tunable weak interaction and its application in SWNT separation.

    Science.gov (United States)

    Pan, Xiaoyong; Chen, Hui; Wang, Wei Zhi; Ng, Siu Choon; Chan-Park, Mary B

    2011-07-21

    This paper explores evidence of an optically mediated interaction that is active in the separation mechanism of certain selective agents through consideration of the contrasting selective behaviors of two conjugated polymers with distinct optical properties. The involvement of a RET-induced intermolecular pairing force is implied by the different illumination response behaviors. The magnitude of this interaction scales with the external stimulus parameter, the illumination irradiance (I), and thus is tunable. This suggests a facile technique to modify the selectivity of polymers toward specific SWNT species by altering the polymer structure to adjust the corresponding intermolecular interaction. This is the first experimental verification and application of a RET-induced intermolecular pairing force to SWNT separation. With this kind of interaction taken into account, reasonable interpretation of some conflicting data, especially PLE maps, can be easily made. The above conclusion can be applied to other substances as long as they are electrically neutral and there is photon-induced RET between them. The significant magnitude of this interaction makes direct manipulation of molecules/particles possible and is expected to have applications in molecular engineering. © 2011 American Chemical Society

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-28

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

  5. A general transformation to canonical form for potentials in pairwise interatomic interactions.

    Science.gov (United States)

    Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

    2015-06-14

    A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

  6. Transport properties in mixtures involving carbon dioxide at low and moderate density: test of several intermolecular potential energies and comparison with experiment

    Science.gov (United States)

    Moghadasi, Jalil; Yousefi, Fakhri; Papari, Mohammad Mehdi; Faghihi, Mohammad Ali; Mohsenipour, Ali Asghar

    2009-09-01

    It is the purpose of this paper to extract unlike intermolecular potential energies of five carbon dioxide-based binary gas mixtures including CO2-He, CO2-Ne, CO2-Ar, CO2-Kr, and CO2-Xe from viscosity data and compare the calculated potentials with other models potential energy reported in literature. Then, dilute transport properties consisting of viscosity, diffusion coefficient, thermal diffusion factor, and thermal conductivity of aforementioned mixtures are calculated from the calculated potential energies and compared with literature data. Rather accurate correlations for the viscosity coefficient of afore-cited mixtures embracing the temperature range 200 K < T < 3273.15 K is reproduced from the present unlike intermolecular potentials energy. Our estimated accuracies for the viscosity are to within ±2%. In addition, the calculated potential energies are used to present smooth correlations for other transport properties. The accuracies of the binary diffusion coefficients are of the order of ±3%. Finally, the unlike interaction energy and the calculated low density viscosity have been employed to calculate high density viscosities using Vesovic-Wakeham method.

  7. Transport properties in mixtures involving carbon dioxide at low and moderate density: test of several intermolecular potential energies and comparison with experiment

    Energy Technology Data Exchange (ETDEWEB)

    Moghadasi, Jalil; Yousefi, Fakhri [Shiraz University, Department of Chemistry, Shiraz (Iran); Papari, Mohammad Mehdi; Faghihi, Mohammad Ali [Shiraz University of Technology, Department of Chemistry, Shiraz (Iran); Mohsenipour, Ali Asghar [University of Waterloo, Department of Chemical Engineering, Waterloo (Canada)

    2009-09-15

    It is the purpose of this paper to extract unlike intermolecular potential energies of five carbon dioxide-based binary gas mixtures including CO{sub 2}-He, CO{sub 2}-Ne, CO{sub 2}-Ar, CO{sub 2}-Kr, and CO{sub 2}-Xe from viscosity data and compare the calculated potentials with other models potential energy reported in literature. Then, dilute transport properties consisting of viscosity, diffusion coefficient, thermal diffusion factor, and thermal conductivity of aforementioned mixtures are calculated from the calculated potential energies and compared with literature data. Rather accurate correlations for the viscosity coefficient of afore-cited mixtures embracing the temperature range 200 Kintermolecular potentials energy. Our estimated accuracies for the viscosity are to within {+-}2%. In addition, the calculated potential energies are used to present smooth correlations for other transport properties. The accuracies of the binary diffusion coefficients are of the order of {+-}3%. Finally, the unlike interaction energy and the calculated low density viscosity have been employed to calculate high density viscosities using Vesovic-Wakeham method. (orig.)

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

    International Nuclear Information System (INIS)

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2015-01-01

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

  9. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    Directory of Open Access Journals (Sweden)

    Peter I. Nagy

    2014-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Francisco Geraldo Barbosa

    2015-12-01

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

  11. Intermolecular Interactions in Ternary Glycerol–Sample–H2O

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, M.L.

    1997-12-01

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

  13. Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and (13)C NMR Chemical Shift Tensors.

    Science.gov (United States)

    Bouzková, Kateřina; Babinský, Martin; Novosadová, Lucie; Marek, Radek

    2013-06-11

    An understanding of the role of intermolecular interactions in crystal formation is essential to control the generation of diverse crystalline forms which is an important concern for pharmaceutical industry. Very recently, we reported a new approach to interpret the relationships between intermolecular hydrogen bonding, redistribution of electron density in the system, and NMR chemical shifts (Babinský et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize a full set of crystal interactions in a sample of anhydrous theobromine as reflected in (13)C NMR chemical shift tensors (CSTs). The important intermolecular contacts are identified by comparing the DFT-calculated NMR CSTs for an isolated theobromine molecule and for clusters composed of several molecules as selected from the available X-ray diffraction data. Furthermore, electron deformation density (EDD) and shielding deformation density (SDD) in the proximity of the nuclei involved in the proposed interactions are calculated and visualized. In addition to the recently reported observations for hydrogen bonding, we focus here particularly on the stacking interactions. Although the principal relations between the EDD and CST for hydrogen bonding (HB) and stacking interactions are similar, the real-space consequences are rather different. Whereas the C-H···X hydrogen bonding influences predominantly and significantly the in-plane principal component of the (13)C CST perpendicular to the HB path and the C═O···H hydrogen bonding modulates both in-plane components of the carbonyl (13)C CST, the stacking modulates the out-of-plane electron density resulting in weak deshielding (2-8 ppm) of both in-plane principal components of the CST and weak shielding (∼ 5 ppm) of the out-of-plane component. The hydrogen-bonding and stacking interactions may add to or subtract from one another to produce total values observed experimentally. On the example of theobromine, we demonstrate

  14. Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines

    Energy Technology Data Exchange (ETDEWEB)

    Dou, Wei-Dong [Department of Physics, Shaoxing University, Shaoxing 312000 (China); Center of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Material Science, City University of Hong Kong, Hong Kong (China); Huang, Shu-Ping [Department of Chemistry, University of South Dakota, Vermillion, South Dakota 57069 (United States); Lee, Chun-Sing, E-mail: apcslee@cityu.edu.hk [Center of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Material Science, City University of Hong Kong, Hong Kong (China)

    2015-10-07

    Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π–π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc and CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.

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

    KAUST Repository

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-06

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

  17. Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity.

    Science.gov (United States)

    Scudieri, Paolo; Musante, Ilaria; Gianotti, Ambra; Moran, Oscar; Galietta, Luis J V

    2016-12-08

    TMEM16A and TMEM16B are plasma membrane proteins with Ca 2+ -dependent Cl - channel function. By replacing the carboxy-terminus of TMEM16A with the equivalent region of TMEM16B, we obtained channels with potentiation of channel activity. Progressive shortening of the chimeric region restricted the "activating domain" to a short sequence close to the last transmembrane domain and led to TMEM16A channels with high activity at very low intracellular Ca 2+ concentrations. To elucidate the molecular mechanism underlying this effect, we carried out experiments based on double chimeras, Forster resonance energy transfer, and intermolecular cross-linking. We also modeled TMEM16A structure using the Nectria haematococca TMEM16 protein as template. Our results indicate that the enhanced activity in chimeric channels is due to altered interaction between the carboxy-terminus and the first intracellular loop in the TMEM16A homo-dimer. Mimicking this perturbation with a small molecule could be the basis for a pharmacological stimulation of TMEM16A-dependent Cl - transport.

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

    DEFF Research Database (Denmark)

    Fernández, Berta; Henriksen, Christian; Farrelly, David

    2013-01-01

    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...

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

    Science.gov (United States)

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

    2018-05-01

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

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

    KAUST Repository

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

    2015-01-01

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

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

    KAUST Repository

    Sutton, Christopher

    2015-06-15

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

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

    Science.gov (United States)

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

    2011-02-15

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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Jiufang Duan

    2015-01-01

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

  5. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

    Science.gov (United States)

    Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

    2012-01-01

    We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

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

    Directory of Open Access Journals (Sweden)

    Macduff O. Okuom

    2013-01-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-01-05

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

  9. Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

    Science.gov (United States)

    da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.

    2015-08-01

    DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  11. Intermolecular potential and rovibrational states of the H2O–D2 complex

    International Nuclear Information System (INIS)

    Avoird, Ad van der; Scribano, Yohann; Faure, Alexandre; Weida, Miles J.; Fair, Joanna R.; Nesbitt, David J.

    2012-01-01

    Graphical abstract: H 2 O–D 2 potential surface and pH 2 O–oD 2 ground state wave function, for planar geometries. Highlights: ► The interaction between H 2 O and H 2 is of great astrophysical interest. ► The rovibrational states of H 2 O–D 2 were computed on an ab initio potential surface. ► Results are compared with the rovibrational states of H 2 O–H 2 computed recently. ► We measured the high-resolution infrared spectrum of H 2 O–D 2 in the H 2 O bend region. ► Comparison with the calculations provides information on H 2 O–H 2 potential surface. - Abstract: A five-dimensional intermolecular potential for H 2 O–D 2 was obtained from the full nine-dimensional ab initio potential surface of Valiron et al. [P. Valiron, M. Wernli, A. Faure, L. Wiesenfeld, C. Rist, S. Kedžuch, J. Noga, J. Chem. Phys. 129 (2008) 134306] by averaging over the ground state vibrational wave functions of H 2 O and D 2 . On this five-dimensional potential with a well depth D e of 232.12 cm −1 we calculated the bound rovibrational levels of H 2 O–D 2 for total angular momentum J = 0–3. The method used to compute the rovibrational levels is similar to a scattering approach—it involves a basis of coupled free rotor wave functions for the hindered internal rotations and the overall rotation of the dimer—while it uses a discrete variable representation of the intermolecular distance coordinate R. The basis was adapted to the permutation symmetry associated with the para/ortho (p/o) nature of both H 2 O and D 2 , as well as to inversion symmetry. As expected, the H 2 O–D 2 dimer is more strongly bound than its H 2 O–H 2 isotopologue [cf. A. van der Avoird, D.J. Nesbitt, J. Chem. Phys. 134 (2011) 044314], with dissociation energies D 0 of 46.10, 50.59, 67.43, and 73.53 cm −1 for pH 2 O–oD 2 , oH 2 O–oD 2 , pH 2 O–pD 2 , and oH 2 O–pD 2 . A rotationally resolved infrared spectrum of H 2 O–D 2 was measured in the frequency region of the H 2 O bend

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

    DEFF Research Database (Denmark)

    Cybulski, Hubert; Henriksen, Christian; Dawes, Richard

    2018-01-01

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

  13. Similarity-transformed perturbation theory on top of truncated local coupled cluster solutions: Theory and applications to intermolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Azar, Richard Julian, E-mail: julianazar2323@berkeley.edu; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2015-05-28

    Your correspondents develop and apply fully nonorthogonal, local-reference perturbation theories describing non-covalent interactions. Our formulations are based on a Löwdin partitioning of the similarity-transformed Hamiltonian into a zeroth-order intramonomer piece (taking local CCSD solutions as its zeroth-order eigenfunction) plus a first-order piece coupling the fragments. If considerations are limited to a single molecule, the proposed intermolecular similarity-transformed perturbation theory represents a frozen-orbital variant of the “(2)”-type theories shown to be competitive with CCSD(T) and of similar cost if all terms are retained. Different restrictions on the zeroth- and first-order amplitudes are explored in the context of large-computation tractability and elucidation of non-local effects in the space of singles and doubles. To accurately approximate CCSD intermolecular interaction energies, a quadratically growing number of variables must be included at zeroth-order.

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

    Directory of Open Access Journals (Sweden)

    O. V. Vashchenko

    2016-07-01

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

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

    International Nuclear Information System (INIS)

    Sheka, E.F.; Natkaniec, I.

    1999-01-01

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

  16. Room temperature ionic liquids: A simple model. Effect of chain length and size of intermolecular potential on critical temperature.

    Science.gov (United States)

    Chapela, Gustavo A; Guzmán, Orlando; Díaz-Herrera, Enrique; del Río, Fernando

    2015-04-21

    A model of a room temperature ionic liquid can be represented as an ion attached to an aliphatic chain mixed with a counter ion. The simple model used in this work is based on a short rigid tangent square well chain with an ion, represented by a hard sphere interacting with a Yukawa potential at the head of the chain, mixed with a counter ion represented as well by a hard sphere interacting with a Yukawa potential of the opposite sign. The length of the chain and the depth of the intermolecular forces are investigated in order to understand which of these factors are responsible for the lowering of the critical temperature. It is the large difference between the ionic and the dispersion potentials which explains this lowering of the critical temperature. Calculation of liquid-vapor equilibrium orthobaric curves is used to estimate the critical points of the model. Vapor pressures are used to obtain an estimate of the triple point of the different models in order to calculate the span of temperatures where they remain a liquid. Surface tensions and interfacial thicknesses are also reported.

  17. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    International Nuclear Information System (INIS)

    Karayel, A.; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

    2015-01-01

    The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule

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

    Science.gov (United States)

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

    2013-06-01

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

  19. Argon intermolecular potential from a measurement of the total scattering cross-section

    International Nuclear Information System (INIS)

    Wong, Y.W.

    1975-01-01

    An inversion method to obtain accurate intermolecular potentials from experimental total cross section measurements is presented. This method is based on the high energy Massey--Smith approximation. The attractive portion of the potential is represented by a multi-parameter spline function and the repulsive part by a Morse function. The best fit potential is obtained by a least squares minimization based on comparison of experimental cross sections with those obtained by a Fourier transform of the reduced Massey--Smith phase shift curve. An experimental method was developed to obtain the total cross sections needed for the above inversion procedure. In this technique, integral cross sections are measured at various resolutions and the total cross section is obtained by extrapolating to infinite resolution. Experimental results obtained for the Ar--Ar system are in excellent agreement with total cross sections calculated using the Barker-Fisher-Watts potential. Inversion of the data to obtain a potential distinguishable from the BFW-potential requires an extension of the method based on the Massey--Smith approximation to permit use of JWKB phase shifts and was not attempted

  20. Symmetry in the polarization expansion for intermolecular forces

    International Nuclear Information System (INIS)

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

    1980-01-01

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

  1. The role of the ion-molecule and molecule-molecule interactions in the formation of the two-ion average force interaction potential

    CERN Document Server

    Ajrian, E A; Sidorenko, S N

    2002-01-01

    The effect of the ion-molecule and intermolecular interactions on the formation of inter-ion average force potentials is investigated within the framework of a classical ion-dipole model of electrolyte solutions. These potentials are shown to possess the Coulomb asymptotics at large distances while in the region of mean distances they reveal creation and disintegration of solvent-shared ion pairs. The calculation results provide a qualitatively authentic physical picture which is experimentally observed in strong electrolytes solutions. In particular, an increased interaction between an ion and a molecule enhances formation of ion pairs in which the ions are separated by one solvent molecule

  2. Electronic transitions and intermolecular forces

    International Nuclear Information System (INIS)

    Hemert, M.C. van.

    1981-01-01

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

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

    International Nuclear Information System (INIS)

    Poulsen, R.; Overgaard, J.; Schulman, A.; Stergaard, C.; Murillo, C.; Spackman, M.; Iversen, B.

    2009-01-01

    Depending on the number of interstitial solvent molecules, n, crystals of the linear chain compound Co3(dipyridylamide)4Cl2·nCH2Cl2 adopt either symmetrical or unsymmetrical metal chain structures. We explore here the possible reasons for such behavior using Hirshfeld surface analysis of intermolecular interactions as well as the charge density determined from 100(1) K X-ray diffraction data on the unsymmetrical complex Co3(dipyridylamide)4Cl2·2.11CH2Cl2, u-1, and crystal structures of u-1 determined from single crystal synchrotron X-ray diffraction data at 20, 150, and 300 K. The new crystal structures are compared with previous structural results on a crystal with slightly different solvent content. This change in solvent content only affects the bond distances to atom Co(3), which are also strongly affected by temperature changes due to a spin crossover transition. Large differences in intermolecular interactions are revealed by the Hirshfeld surface analysis between symmetrical (s-1) and unsymmetrical (u-1) crystal solvates, suggesting that the molecular isomerism is strongly influenced by crystal packing effects. Topological analysis of the static electron density of u-1 suggests that there is direct metal-metal bonding for both the shorter Co(1)-Co(2) and the longer Co(2)-Co(3) contact. The approximate description of the system as a (Co2)2+-dimer and an isolated Co2+-ion is reflected in the character of the metal-ligand interactions, which are more ionic for the isolated Co(3) atom, and the topological charges Co(1)+0.50, Co(2)+0.77, and Co(3)+1.36. The two termini of u-1 are found to be very different, both in terms of structural surroundings as well as topology. The central Co(2) atom is similar to a cobalt atom in a tetragonally distorted octahedral environment resulting in preferred occupancy in the t2g orbitals. The Co(1) atom has significant deformation in the xz and yz planes (z along the chain axis, x and y toward ligands) reflecting covalent

  4. Intermolecular potential and rovibrational states of the H{sub 2}O-D{sub 2} complex

    Energy Technology Data Exchange (ETDEWEB)

    Avoird, Ad van der, E-mail: A.vanderAvoird@theochem.ru.nl [Theoretical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Scribano, Yohann [Laboratoire Interdisciplinaire Carnot de Bourgogne-UMR 5209, CNRS-Universite de Bourgogne, 9 Av. Alain Savary, B.P. 47870, F-21078 Dijon Cedex (France); Faure, Alexandre [UJF-Grenoble 1/CNRS, Institut de Planetologie et d' Astrophysique de Grenoble (IPAG) UMR 5274, Grenoble F-38041 (France); Weida, Miles J. [Daylight Solutions, 15378 Avenue of Science, San Diego, CA 92128 (United States); Fair, Joanna R. [Department of Radiology, MSC10 5530, 1 University of New Mexico, Albuquerque, NM 87131-0001 (United States); Nesbitt, David J. [JILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440 (United States)

    2012-05-03

    Graphical abstract: H{sub 2}O-D{sub 2} potential surface and pH{sub 2}O-oD{sub 2} ground state wave function, for planar geometries. Highlights: Black-Right-Pointing-Pointer The interaction between H{sub 2}O and H{sub 2} is of great astrophysical interest. Black-Right-Pointing-Pointer The rovibrational states of H{sub 2}O-D{sub 2} were computed on an ab initio potential surface. Black-Right-Pointing-Pointer Results are compared with the rovibrational states of H{sub 2}O-H{sub 2} computed recently. Black-Right-Pointing-Pointer We measured the high-resolution infrared spectrum of H{sub 2}O-D{sub 2} in the H{sub 2}O bend region. Black-Right-Pointing-Pointer Comparison with the calculations provides information on H{sub 2}O-H{sub 2} potential surface. - Abstract: A five-dimensional intermolecular potential for H{sub 2}O-D{sub 2} was obtained from the full nine-dimensional ab initio potential surface of Valiron et al. [P. Valiron, M. Wernli, A. Faure, L. Wiesenfeld, C. Rist, S. Kedzuch, J. Noga, J. Chem. Phys. 129 (2008) 134306] by averaging over the ground state vibrational wave functions of H{sub 2}O and D{sub 2}. On this five-dimensional potential with a well depth D{sub e} of 232.12 cm{sup -1} we calculated the bound rovibrational levels of H{sub 2}O-D{sub 2} for total angular momentum J = 0-3. The method used to compute the rovibrational levels is similar to a scattering approach-it involves a basis of coupled free rotor wave functions for the hindered internal rotations and the overall rotation of the dimer-while it uses a discrete variable representation of the intermolecular distance coordinate R. The basis was adapted to the permutation symmetry associated with the para/ortho (p/o) nature of both H{sub 2}O and D{sub 2}, as well as to inversion symmetry. As expected, the H{sub 2}O-D{sub 2} dimer is more strongly bound than its H{sub 2}O-H{sub 2} isotopologue [cf. A. van der Avoird, D.J. Nesbitt, J. Chem. Phys. 134 (2011) 044314], with dissociation energies D

  5. Investigation on intermolecular interaction between berberine and β-cyclodextrin by 2D UV-Vis asynchronous spectra.

    Science.gov (United States)

    He, Anqi; Kang, Xiaoyan; Xu, Yizhuang; Noda, Isao; Ozaki, Yukihiro; Wu, Jinguang

    2017-10-05

    The interaction between berberine chloride and β-cyclodextrin (β-CyD) is investigated via 2D asynchronous UV-Vis spectrum. The occurrence of cross peaks around (420nm, 420nm) in 2D asynchronous spectrum reveals that specific intermolecular interaction indeed exists between berberine chloride and β-CyD. In spite of the difficulty caused by overlapping of cross peaks, we manage to confirm that the 420nm band of berberine undergoes a red-shift, and its bandwidth decreases under the interaction with β-CyD. The red-shift of the 420nm band that can be assigned to n-π* transition indicates the environment of berberine becomes more hydrophobic. The above spectral behavior is helpful in understanding why the solubility of berberine is enhanced by β-CyD. Copyright © 2017. Published by Elsevier B.V.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-01

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

  7. Intermolecular spectroscopy

    International Nuclear Information System (INIS)

    Gelbart, W.M.

    1980-01-01

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

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

    Science.gov (United States)

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

    2014-03-01

    The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2018-04-19

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

  12. Proper construction of ab initio global potential surfaces with accurate long-range interactions

    International Nuclear Information System (INIS)

    Ho, Tak-San; Rabitz, Herschel

    2000-01-01

    An efficient procedure based on the reproducing kernel Hilbert space interpolation method is presented for constructing intermolecular potential energy surfaces (PES) using not only calculated ab initio data but also a priori information on long-range interactions. Explicitly, use of the reciprocal power reproducing kernel on the semiinfinite interval [0,∞) yields a set of exact linear relations between dispersion (multipolar) coefficients and PES data points at finite internuclear separations. Consequently, given a combined set of ab initio data and the values of dispersion (multipolar) coefficients, the potential interpolation problem subject to long-range interaction constraints can be solved to render globally smooth, asymptotically accurate ab initio potential energy surfaces. Very good results have been obtained for the one-dimensional He-He potential curve and the two-dimensional Ne-CO PES. The construction of the Ne-CO PES was facilitated by invoking a new reproducing kernel for the angular coordinate based on the optimally stable and shape-preserving Bernstein basis functions. (c) 2000 American Institute of Physics

  13. Temperature-dependent interaction potential between NF3 molecules and thermophysical properties of gaseous NF3

    International Nuclear Information System (INIS)

    Damyanova, M; Balabanova, E; Hohm, U

    2014-01-01

    A temperature-dependent effective intermolecular interaction potential is applied to describe the interaction between two nitrogen fluoride (NF 3 ) molecules in gas phase. To this end, a spherically-symmetric (n-6) Lennard-Jones temperature-dependent potential (LJTDP) is used. The (n-6) LJTDP takes into account the influence of vibrational excitation of the molecules on the potential parameters, namely, the equilibrium distance r m and the potential well depth ε. The potential parameters at T = 0 K were obtained from the very small amount of existing thermophysical equilibrium and transport properties of low-density NF 3 gas. Fitting formulae are tabulated for a fast and reliable prediction of the thermophysical properties and potential parameters in the temperature range between 200 K and 1200 K. A comparison is also presented between our estimates for some thermophysical properties of the NF 3 gas with the available experimental and calculated data.

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

    Directory of Open Access Journals (Sweden)

    Konczak L

    2016-11-01

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

  15. 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)

    Hansen, Flemming Yssing; Alldredge, G. P.; Bruch, L. W.

    1985-01-01

    and gives a repulsive rather than an attractive electrostatic interaction at typical intermolecular distances. In the local multipole model, the atom-site dipoles give the largest contribution to both the molecular quadrupole moment and the intermolecular interaction. The Journal of Chemical Physics...

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

    Science.gov (United States)

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

    2017-07-20

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

  17. Crystal structures of 4-chloropyridine-2-carbonitrile and 6-chloropyridine-2-carbonitrile exhibit different intermolecular π-stacking, C—H...Nnitrile and C—H...Npyridine interactions

    Directory of Open Access Journals (Sweden)

    Matthew J. Montgomery

    2015-07-01

    Full Text Available The two title compounds are isomers of C6H3ClN2 containing a pyridine ring, a nitrile group, and a chloro substituent. The molecules of each compound pack together in the solid state with offset face-to-face π-stacking, and intermolecular C—H...Nnitrile and C—H...Npyridine interactions. 4-Chloropyridine-2-carbonitrile, (I, exhibits pairwise centrosymmetric head-to-head C—H...Nnitrile and C—H...Npyridine interactions, forming one-dimensional chains, which are π-stacked in an offset face-to-face fashion. The intermolecular packing of the isomeric 6-chloropyridine-2-carbonitrile, (II, which differs only in the position of the chloro substituent on the pyridine ring, exhibits head-to-tail C—H...Nnitrile and C—H...Npyridine interactions, forming two-dimensional sheets which are π-stacked in an offset face-to-face fashion. In contrast to (I, the offset face-to-face π-stacking in (II is formed between molecules with alternating orientations of the chloro and nitrile substituents.

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2017-06-08

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

  20. Influence of pressure on the crystallization of systems characterized by different intermolecular attraction

    Science.gov (United States)

    Koperwas, K.; Affouard, F.; Gerges, J.; Valdes, L.-C.; Adrjanowicz, K.; Paluch, M.

    2017-12-01

    In this paper, we examine, in terms of the classical nucleation theory, how the strengthening of the attractive intermolecular interactions influences the crystallization process for systems like Lennard-Jones at different isobaric conditions. For this purpose, we modify the standard Lennard-Jones potential, and as a result, we obtain three different systems characterized by various strengths of attractive potentials occurring between molecules, which are in direct relationship to the physical quantities describing molecules, e.g., its polarizability or dipole moment. Based on performed analysis, we demonstrate that the molecular attraction primarily impacts the thermodynamics of the interface between liquid and crystal. This is reflected in the behavior of nucleation and overall crystallization rates during compression of the system.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-03-15

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

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

    International Nuclear Information System (INIS)

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

    1974-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  4. Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods.

    Science.gov (United States)

    Christensen, Anders S; Kromann, Jimmy C; Jensen, Jan H; Cui, Qiang

    2017-10-28

    To facilitate further development of approximate quantum mechanical methods for condensed phase applications, we present a new benchmark dataset of intermolecular interaction energies in the solution phase for a set of 15 dimers, each containing one charged monomer. The reference interaction energy in solution is computed via a thermodynamic cycle that integrates dimer binding energy in the gas phase at the coupled cluster level and solute-solvent interaction with density functional theory; the estimated uncertainty of such calculated interaction energy is ±1.5 kcal/mol. The dataset is used to benchmark the performance of a set of semi-empirical quantum mechanical (SQM) methods that include DFTB3-D3, DFTB3/CPE-D3, OM2-D3, PM6-D3, PM6-D3H+, and PM7 as well as the HF-3c method. We find that while all tested SQM methods tend to underestimate binding energies in the gas phase with a root-mean-squared error (RMSE) of 2-5 kcal/mol, they overestimate binding energies in the solution phase with an RMSE of 3-4 kcal/mol, with the exception of DFTB3/CPE-D3 and OM2-D3, for which the systematic deviation is less pronounced. In addition, we find that HF-3c systematically overestimates binding energies in both gas and solution phases. As most approximate QM methods are parametrized and evaluated using data measured or calculated in the gas phase, the dataset represents an important first step toward calibrating QM based methods for application in the condensed phase where polarization and exchange repulsion need to be treated in a balanced fashion.

  5. Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods

    Science.gov (United States)

    Christensen, Anders S.; Kromann, Jimmy C.; Jensen, Jan H.; Cui, Qiang

    2017-10-01

    To facilitate further development of approximate quantum mechanical methods for condensed phase applications, we present a new benchmark dataset of intermolecular interaction energies in the solution phase for a set of 15 dimers, each containing one charged monomer. The reference interaction energy in solution is computed via a thermodynamic cycle that integrates dimer binding energy in the gas phase at the coupled cluster level and solute-solvent interaction with density functional theory; the estimated uncertainty of such calculated interaction energy is ±1.5 kcal/mol. The dataset is used to benchmark the performance of a set of semi-empirical quantum mechanical (SQM) methods that include DFTB3-D3, DFTB3/CPE-D3, OM2-D3, PM6-D3, PM6-D3H+, and PM7 as well as the HF-3c method. We find that while all tested SQM methods tend to underestimate binding energies in the gas phase with a root-mean-squared error (RMSE) of 2-5 kcal/mol, they overestimate binding energies in the solution phase with an RMSE of 3-4 kcal/mol, with the exception of DFTB3/CPE-D3 and OM2-D3, for which the systematic deviation is less pronounced. In addition, we find that HF-3c systematically overestimates binding energies in both gas and solution phases. As most approximate QM methods are parametrized and evaluated using data measured or calculated in the gas phase, the dataset represents an important first step toward calibrating QM based methods for application in the condensed phase where polarization and exchange repulsion need to be treated in a balanced fashion.

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

    DEFF Research Database (Denmark)

    Hanni, Matti; Lantto, Perttu; Ilias, Miroslav

    2007-01-01

    Relativistic effects on the 129Xe nuclear magnetic resonance shielding and 131Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe2 system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular...... interaction-induced binary chemical shift d, the anisotropy of the shielding tensor ?s, and the NQC constant along the internuclear axis ?ll are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full...... is obtained for d and ?s in Xe2. For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other...

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

    Science.gov (United States)

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

    2018-04-16

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

  8. Desensitization of metastable intermolecular composites

    Science.gov (United States)

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

    2011-04-26

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

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

    Directory of Open Access Journals (Sweden)

    GAO Shan

    2017-12-01

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

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

    International Nuclear Information System (INIS)

    Tang, Chun; Clore, G. Marius

    2006-01-01

    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 δ-methyl groups of isoleucine, while the other component is uniformly 13 C-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 IIA Glc -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 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

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

    CERN Document Server

    Lukashov, Sergey; Pravilov, Anatoly

    2018-01-01

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

  12. Quantum mechanical calculations on weakly interacting complexes

    NARCIS (Netherlands)

    Heijmen, T.G.A.

    1998-01-01

    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

  13. Intermolecular potential energy surface and thermophysical properties of propane.

    Science.gov (United States)

    Hellmann, Robert

    2017-03-21

    A six-dimensional potential energy surface (PES) for the interaction of two rigid propane molecules was determined from supermolecular ab initio calculations up to the coupled cluster with single, double, and perturbative triple excitations level of theory for 9452 configurations. An analytical site-site potential function with 14 sites per molecule was fitted to the calculated interaction energies. To validate the analytical PES, the second virial coefficient and the dilute gas shear viscosity and thermal conductivity of propane were computed. The dispersion part of the potential function was slightly adjusted such that quantitative agreement with the most accurate experimental data for the second virial coefficient at room temperature was achieved. The adjusted PES yields values for the three properties that are in very good agreement with the best experimental data at all temperatures.

  14. Intermolecular and surface forces

    CERN Document Server

    Israelachvili, Jacob N

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chun; Clore, G. Marius [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: mariusc@intra.niddk.nih.gov

    2006-09-15

    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 {delta}-methyl groups of isoleucine, while the other component is uniformly {sup 13}C-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 IIA{sup Glc}-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 atomic positions) with an overall backbone accuracy of {approx}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.

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

    International Nuclear Information System (INIS)

    Tsui, H.H.Y.

    2001-01-01

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

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

    Science.gov (United States)

    Kreck, Cara A; Mancera, Ricardo L

    2014-02-20

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

  19. The interaction of MnH(X 7Sigma+) with He: ab initio potential energy surface and bound states.

    Science.gov (United States)

    Turpin, Florence; Halvick, Philippe; Stoecklin, Thierry

    2010-06-07

    The potential energy surface of the ground state of the He-MnH(X (7)Sigma(+)) van der Waals complex is presented. Within the supermolecular approach of intermolecular energy calculations, a grid of ab initio points was computed at the multireference configuration interaction level using the aug-cc-pVQZ basis set for helium and hydrogen and the relativistic aug-cc-pVQZ-DK basis set for manganese. The potential energy surface was then fitted to a global analytical form which main features are discussed. As a first application of this potential energy surface, we present accurate calculations of bound energy levels of the (3)He-MnH and (4)He-MnH complexes.

  20. The interaction of MnH(X 7Σ+) with He: Ab initio potential energy surface and bound states

    Science.gov (United States)

    Turpin, Florence; Halvick, Philippe; Stoecklin, Thierry

    2010-06-01

    The potential energy surface of the ground state of the He-MnH(X Σ7+) van der Waals complex is presented. Within the supermolecular approach of intermolecular energy calculations, a grid of ab initio points was computed at the multireference configuration interaction level using the aug-cc-pVQZ basis set for helium and hydrogen and the relativistic aug-cc-pVQZ-DK basis set for manganese. The potential energy surface was then fitted to a global analytical form which main features are discussed. As a first application of this potential energy surface, we present accurate calculations of bound energy levels of the H3e-MnH and H4e-MnH complexes.

  1. Direct measurements of intermolecular forces by chemical force microscopy

    Science.gov (United States)

    Vezenov, Dmitri Vitalievich

    1999-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Yang-Hui; Liu, Qing-Ling; Yang, Li-Jing; Ling, Yang; Wang, Wei; Sun, Bai-Wang, E-mail: chmsunbw@seu.edu.cn

    2015-02-15

    A new spin crossover coordination polymer (SCO-CPs) of Fe(II)-4,4′-bipyridine (4,4′-bipy) family: (Fe(4,4′-bipy){sub 2}(H{sub 2}O){sub 2})·(4,4′-bipy)· 8(H{sub 2}O)·2(ClO{sub 4}) (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 π…π 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) (H{sub 2}O){sub 2} (NCS){sub 2})·4,4′-bipy, 1 and (Fe(4,4′-bipy){sub 2}(NCS){sub 2})·mSolv, 2) through Hirshfeld surfaces analysis, which revealed that the low ligand field strength (NCS{sup −}) 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 π…π packing interactions) make for the LS (low-spin) state. - Highlights: ●A new member of Fe(||)-4,4′-bipy family has been prepared. ●It displays half spin transitions tuned by ligand field and intermolecular interactions. ●We have made a detailed comparison of this new member with two other analogous complexes.

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

    Science.gov (United States)

    Beauchamp, Guy

    2008-10-23

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

  4. Desensitization and recovery of metastable intermolecular composites

    Science.gov (United States)

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

    2010-09-07

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

  5. Supramolecular interactions in the solid state

    Directory of Open Access Journals (Sweden)

    Giuseppe Resnati

    2015-11-01

    Full Text Available In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1 an overview and historical review of halogen bonding; (2 exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3 the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4 strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.

  6. Ab initio calculation of intermolecular potentials for dimer Cl_2-Cl_2 and prediction of second virial coefficients

    International Nuclear Information System (INIS)

    Nguyen Thanh Duoc; Nguyen Thi Ai Nhung; Tran Duong; Pham Van Tat

    2015-01-01

    The results presented in this paper are the ab initio intermolecular potentials and the second virial coefficient, B_2 (T) of the dimer Cl_2-Cl_2. These ab initio potentials were proposed by the quantum chemical calculations at high level of theory CCSD(T) with basis sets of Dunning valence correlation-consistent aug-cc-pVmZ (m = 2, 3); these results were extrapolated to complete basis set limit aug-cc-pV23Z. The ab initio energies of complete basis set limit aug-cc-pV23Z resulted from the exponential extrapolation were used to construct the 5-site pair potential functions. The second virial coefficients for this dimer were predicted from those with four-dimensional integration. The second virial coefficients were also corrected to first-order quantum effects. The results turn out to be in good agreement with experimental data, if available, or with those from empirical correlation. The quality of ab initio 5-site potentials proved the reliability for prediction of molecular thermodynamic properties. (author)

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2017-04-01

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

  9. Collision-induced spectroscopy with long-range intermolecular interactions: A diagrammatic representation and the invariant form of the induced properties

    International Nuclear Information System (INIS)

    Kouzov, A. P.; Chrysos, M.; Rachet, F.; Egorova, N. I.

    2006-01-01

    Collision-induced properties of two interacting molecules a and b are derived by means of a general diagrammatic method involving M molecule-molecule and N photon-molecule couplings. The method is an extension of previous graphical treatments of nonlinear optics because it exhaustively determines interaction-induced polarization mechanisms in a trustworthy and handy fashion. Here we focus on long-range intermolecular interactions. Retardation effects are neglected. A fully quantum-mechanical treatment of the molecules is made whereas second quantization for the electromagnetic field, in the nonrelativistic approximation, is implicitly applied. The collision-induced absorption, Raman, and hyper-Raman processes are viewed and studied, through guiding examples, as specific cases N=1, 2, and 3, respectively. In Raman (N=2), the standard first-order (M=1) dipole-induced dipole term of the incremental polarizability, Δα, is the result of a coupling of the two photons with distinct molecules, a and b, which perturb each other via a dipole-dipole mechanism. Rather, when the two photons interact with the same molecule, a or b, the (N=2, M=1) graphs predict the occurrence of a nonlinear polarization mechanism. The latter is expected to contribute substantially to the collision-induced Raman bands by certain molecular gases

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

    Science.gov (United States)

    Wernsdorfer, W.; Bhaduri, S.; Vinslava, A.; Christou, G.

    2005-12-01

    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, and (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 occurs which does not quench tunneling. An applied transverse field can increase the ordering rate. Spin-spin cross-relaxations, mediated by dipolar and weak exchange interactions, are proposed to explain additional quantum steps.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  12. Intermolecular potential energy surface and thermophysical properties of ethylene oxide.

    Science.gov (United States)

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

    2014-10-28

    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.

  13. Data in support of intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures

    Directory of Open Access Journals (Sweden)

    Takayuki Odahara

    2016-06-01

    Full Text Available The data provide information in support of the research article, “Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures” [1]. The data regarding variation of absorption spectra is used as an indicator of the duration of Rp. viridis PRU and RC, Rb. sphaeroides RC and LH2, and Rb. capsulatus LH2 in the native state in the presence of NaCl/polyethylene glycol (PEG mixture. The data about minimum concentrations of salt and PEG whose aqueous phases are mutually separated presents information on additional influence of Tris buffer and N-octyl-β-d-glucoside on the salt–PEG phase separation.

  14. 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)

    Power, E.A.; Thirunamachandran, T.

    1993-01-01

    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')/λ. 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

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

    Science.gov (United States)

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

    2014-10-07

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

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

    International Nuclear Information System (INIS)

    Heßelmann, Andreas; Korona, Tatiana

    2014-01-01

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

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

    Science.gov (United States)

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

    2007-10-28

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

  18. Effective intermolecular potential and critical point for C60 molecule

    Science.gov (United States)

    Ramos, J. Eloy

    2017-07-01

    The approximate nonconformal (ANC) theory is applied to the C60 molecule. A new binary potential function is developed for C60, which has three parameters only and is obtained by averaging the site-site carbon interactions on the surface of two C60 molecules. It is shown that the C60 molecule follows, to a good approximation, the corresponding states principle with n-C8H18, n-C4F10 and n-C5F12. The critical point of C60 is estimated in two ways: first by applying the corresponding states principle under the framework of the ANC theory, and then by using previous computer simulations. The critical parameters obtained by applying the corresponding states principle, although very different from those reported in the literature, are consistent with the previous results of the ANC theory. It is shown that the Girifalco potential does not correspond to an average of the site-site carbon-carbon interaction.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  20. Cooperativity effect involving drug-DNA/RNA intermolecular interaction: A B3LYP-D3 and MP2 theoretical investigation on ketoprofen⋯cytosine⋯H2O system.

    Science.gov (United States)

    Zhen, Jun-Ping; Wei, Xiao-Chun; Shi, Wen-Jing; Huang, Zhu-Yuan; Jin, Bo; Zhou, Yu-Kun

    2017-11-14

    In order to examine the origin of the drug action and design new DNA/RNA-targeted drugs, the cooperativity effect involving drug-DNA/RNA intermolecular interaction in ketoprofen⋯cytosine⋯H 2 O ternary system were investigated by the B3LYP, B3LYP-D3, and MP2 methods with the 6-311++G(2d,p) basis set. The thermodynamic cooperativity was also evaluated at 310.15 K. The N-H⋯O, O-H⋯O, O-H⋯N, C-H⋯N, and C-H⋯O H bonds coexist in ternary complexes. The intermolecular interactions obtained by B3LYP-D3 are close to those calculated by MP2. The steric effects and van der Waals interactions have little influence on the cooperativity effects. The anti-cooperativity effect in ket⋯cyt⋯H 2 O is far more notable than the cooperativity effect, and the stability of the cyclic structure with anti-cooperativity effect is higher than that of the linear structure with cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that, in the presence of H 2 O, the anti-cooperativity effect plays a dominant role in the drug-DNA/RNA interaction, and the nature of the hydration in the binding of drugs to DNA/RNA bases is the H-bonding anti-cooperativity effect. Furthermore, the drug always links simultaneously with DNA/RNA base and H 2 O, and only in this way can the biological activity of drugs play a role. In most cases, the enthalpy change is the major factor driving the cooperativity, as is different from most of biomacromolecule complexes.

  1. Molecular self assembly and chiral recognition of copper octacyanophthalocyanine on Au(111): Interplay of intermolecular and molecule-substrate interactions.

    Science.gov (United States)

    Sk, Rejaul; Dhara, Barun; Miller, Joel; Deshpande, Aparna

    Submolecular resolution scanning tunneling microscopy (STM) of copper octacyanophthalocyanine, CuPc(CN)8, at 77 K demonstrates that these achiral molecules form a two dimensional (2D) tetramer-based self-assembly upon evaporation onto an atomically flat Au(111) substrate. They assemble in two different structurally chiral configurations upon adsorption on Au(111). Scanning tunneling spectroscopy (STS),acquired at 77 K, unveils the HOMO and LUMO energy levels of this self-assembly. Voltage dependent STM images show that each molecule in both the structurally chiral configurations individually becomes chiral by breaking the mirror symmetry due to the enhanced intermolecular dipolar coupling interaction at the LUMO energy while the individual molecules remain achiral at the HOMO energy and within the HOMO-LUMO gap. At the LUMO energy, the handedness of the each chiral molecule is decided by the direction of the dipolar coupling interaction in the tetramer unit cell. This preference for LUMO energy indicates that this chirality is purely electronic in nature and it manifests on top of the organizational chirality that is present in the self-assembly independent of the orbital energy. Supported by IISER Pune and DAE-BRNS, India (Project No. 2011/20/37C/17/BRNS).

  2. A computer simulation of a potential derived from the gay-berne potential for lattice model

    Directory of Open Access Journals (Sweden)

    Habtamu Zewdie

    2000-06-01

    Full Text Available The lattice model of elongated molecules interacting via a potential derived from the Gay-Berne pair potential is proposed. We made a systematic study of the effect of varying the molecular elongation and intermolecular vector orientation dependence of the pair potential on the thermodynamic as well as the structural properties of liquid crystals. A Monte Carlo simulations of molecules placed at the site of a simple cubic lattice and interacting via the modified Gay-Berne potential with its nearest neighbours is performed. The internal energy, heat capacity, angular pair correlation function and scalar order parameter are obtained. The results are compared against predictions of molecular field theory, experimental results and that of other related simulations wherever possible. It is shown that for more elongated molecules the nematic-isotropic transition becomes stronger first order transition. For a given molecular elongation as the intermolecular vector orientation dependence becomes larger the nematic-isotropic transition becomes a stronger first order transition as measured by the rate of change of the order parameter and the divergence of the heat capacity. Scaling the potential well seems to have dramatic change on the effect of the potential well anisotropy on trends of nematic-isotropic transition temperature and divergence of the heat capacity. It is shown that the behaviour of many nematics can be described by proposed model with the elongation ratio of molecules and potential well anisotropy ranging from 3 to 5.

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

    Science.gov (United States)

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

    2018-05-01

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

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

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Hansen, Jakob L; Sheikh, Søren P

    2002-01-01

    -induced intermolecular movements in the CaR homodimer using the new bioluminescence resonance energy transfer technique, BRET2, which is based on the transference of energy from Renilla luciferase (Rluc) to the green fluorescent protein mutant GFP2. We tagged CaR with Rluc and GFP2 at different intracellular locations...

  5. A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein–nucleic acid complexes

    International Nuclear Information System (INIS)

    Anderson, Kurtis M.; Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani; Gorenstein, David G.; Iwahara, Junji

    2015-01-01

    Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH 3 + groups forming the intermolecular ion pairs. A characteristic change in their 1 H and 15 N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain 15 N and DNA phosphorodithiaote 31 P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well

  6. Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

    Science.gov (United States)

    Bereau, Tristan; DiStasio, Robert A.; Tkatchenko, Alexandre; von Lilienfeld, O. Anatole

    2018-06-01

    Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning (ML), coined IPML, which is transferable across small neutral organic and biologically relevant molecules. ML models provide on-the-fly predictions for environment-dependent local atomic properties: electrostatic multipole coefficients (significant error reduction compared to previously reported), the population and decay rate of valence atomic densities, and polarizabilities across conformations and chemical compositions of H, C, N, and O atoms. These parameters enable accurate calculations of intermolecular contributions—electrostatics, charge penetration, repulsion, induction/polarization, and many-body dispersion. Unlike other potentials, this model is transferable in its ability to handle new molecules and conformations without explicit prior parametrization: All local atomic properties are predicted from ML, leaving only eight global parameters—optimized once and for all across compounds. We validate IPML on various gas-phase dimers at and away from equilibrium separation, where we obtain mean absolute errors between 0.4 and 0.7 kcal/mol for several chemically and conformationally diverse datasets representative of non-covalent interactions in biologically relevant molecules. We further focus on hydrogen-bonded complexes—essential but challenging due to their directional nature—where datasets of DNA base pairs and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and as a first look, we consider IPML for denser systems: water clusters, supramolecular host-guest complexes, and the benzene crystal.

  7. Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification.

    Science.gov (United States)

    Xu, Jianguo; Zheng, Tingting; Le, Jingqing; Jia, Lee

    2017-11-20

    Occurrence and application of oligonucleotide probes have promoted great progress in the biochemical analysis field due to their unique biological and chemical properties. In this work, a long-stem shaped multifunctional molecular beacon (LS-MMB) that is responsive to a cancer-related gene, p53, is well-prepared. By designing the probe with long-paired bases at its two ends and short-paired bases between the middle region and the 3' end, the LS-MMB is intelligently endowed with the ability to recognize the target analyte, serve as the polymerization primer/template, and signal the hybridization event synchronously, which is distinctly advantageous over the traditional molecular beacons (MBs). Moreover, it is excitingly found that the LS-MMB can be employed to exert intramolecular and intermolecular interactions for strand displacement amplification (SDA) without the involvement of any assistant probes; this therapy results in a really easy and rapid sensing system that provides an extremely low background noise and high target output signal. In this case, an excellent sensitivity and specificity to detect target gene down to picomolar level and resolution to even one nucleotide variation are achieved, respectively. In addition, the application potential for real genomic DNA analysis is realized. We envision that the probe of LS-MMB can act as a universal platform for biosensing and biomedical research.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-01

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

  9. Structural modeling and intermolecular correlation of liquid chlorine dioxide

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  10. A Polarizable and Transferable PHAST CO 2 Potential for Materials Simulation

    KAUST Repository

    Mullen, Ashley L.

    2013-12-10

    Reliable PHAST (Potentials with High Accuracy Speed and Transferability) intermolecular potential energy functions for CO2 have been developed from first principles for use in heterogeneous systems, including one with explicit polarization. The intermolecular potentials have been expressed in a transferable form and parametrized from nearly exact electronic structure calculations. Models with and without explicit many-body polarization effects, known to be important in simulation of interfacial processes, are constructed. The models have been validated on pressure-density isotherms of bulk CO 2 and adsorption in three metal-organic framework (MOF) materials. The present models appear to offer advantages over high quality fluid/liquid state potentials in describing CO2 interactions in interfacial environments where sorbates adopt orientations not commonly explored in bulk fluids. Thus, the nonpolar CO2-PHAST and polarizable CO 2-PHAST* potentials are recommended for materials/interfacial simulations. © 2013 American Chemical Society.

  11. Ab initio intermolecular potential energy surface and thermophysical properties of hydrogen sulfide.

    Science.gov (United States)

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

    2011-08-14

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid hydrogen sulfide molecules was determined from high-level quantum-mechanical ab initio computations. A total of 4016 points for 405 different angular orientations of two molecules were calculated utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory and extrapolating the calculated interaction energies to the complete basis set limit. An analytical site-site potential function with eleven sites per hydrogen sulfide molecule was fitted to the interaction energies. The PES has been validated by computing the second pressure virial coefficient, shear viscosity, thermal conductivity and comparing with the available experimental data. The calculated values of volume viscosity were not used to validate the potential as the low accuracy of the available data precluded such an approach. The second pressure virial coefficient was evaluated by means of the Takahashi and Imada approach, while the transport properties, in the dilute limit, were evaluated by utilizing the classical trajectory method. In general, the agreement with the primary experimental data is within the experimental error for temperatures higher than 300 K. For lower temperatures the lack of reliable data indicates that the values of the second pressure virial coefficient and of the transport properties calculated in this work are currently the most accurate estimates for the thermophysical properties of hydrogen sulfide.

  12. A chemical approach for site-specific identification of NMR signals from protein side-chain NH{sub 3}{sup +} groups forming intermolecular ion pairs in protein–nucleic acid complexes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Kurtis M. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States); Gorenstein, David G. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Iwahara, Junji, E-mail: juiwahar@utmb.edu, E-mail: j.iwahara@utmb.edu [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States)

    2015-05-15

    Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH{sub 3}{sup +} groups forming the intermolecular ion pairs. A characteristic change in their {sup 1}H and {sup 15}N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain {sup 15}N and DNA phosphorodithiaote {sup 31}P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well.

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

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, J.; Wallin Mahler Andersen, Denise

    2014-01-01

    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...

  14. Intermolecular cleavage by UmuD-like mutagenesis proteins

    Science.gov (United States)

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

    1998-01-01

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

  15. 2010 Atomic & Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Todd Martinez

    2010-07-23

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

  16. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix.

    Science.gov (United States)

    Pley, H W; Flaherty, K M; McKay, D B

    1994-11-03

    In large structured RNAs, RNA hairpins in which the strands of the duplex stem are connected by a tetraloop of the consensus sequence 5'-GNRA (where N is any nucleotide, and R is either G or A) are unusually frequent. In group I introns there is a covariation in sequence between nucleotides in the third and fourth positions of the loop with specific distant base pairs in putative RNA duplex stems: GNAA loops correlate with successive 5'-C-C.G-C base pairs in stems, whereas GNGA loops correlate with 5'-C-U.G-A. This has led to the suggestion that GNRA tetraloops may be involved in specific long-range tertiary interactions, with each A in position 3 or 4 of the loop interacting with a C-G base pair in the duplex, and G in position 3 interacting with a U-A base pair. This idea is supported experimentally for the GAAA loop of the P5b extension of the group I intron of Tetrahymena thermophila and the L9 GUGA terminal loop of the td intron of bacteriophage T4 (ref. 4). NMR has revealed the overall structure of the tetraloop for 12-nucleotide hairpins with GCAA and GAAA loops and models have been proposed for the interaction of GNRA tetraloops with base pairs in the minor groove of A-form RNA. Here we describe the crystal structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. The interactions we observe correlate with the specificity of GNRA tetraloops inferred from phylogenetic studies, suggesting that this complex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs.

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

    Science.gov (United States)

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

    2008-12-31

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

  18. Conformations and Intermolecular Interactions in Cellulose/Silk Fibroin Blend Films: A Solid-State NMR Perspective.

    Science.gov (United States)

    Tian, Donglin; Li, Tao; Zhang, Rongchun; Wu, Qiang; Chen, Tiehong; Sun, Pingchuan; Ramamoorthy, Ayyalusamy

    2017-06-29

    Fabricating materials with excellent mechanical performance from the natural renewable and degradable biopolymers has drawn significant attention in recent decades due to the environmental concerns and energy crisis. As two of the most promising substitutes of synthetic polymers, silk fibroin (SF), and cellulose, have been widely used in the field of textile, biomedicine, biotechnology, etc. Particularly, the cellulose/SF blend film exhibits better strength and toughness than that of regenerated cellulose film. Herein, this study is aimed to understand the molecular origin of the enhanced mechanical properties for the cellulose/SF blend film, using solid-state NMR as a main tool to investigate the conformational changes, intermolecular interactions between cellulose and SF and the water organization. It is found that the content of the β-sheet structure is increased in the cellulose/SF blend film with respect to the regenerated SF film, accompanied by the reduction of the content of random coil structures. In addition, the strong hydrogen bonding interaction between the SF and cellulose is clearly elucidated by the two-dimensional (2D) 1 H- 13 C heteronuclear correlation (HETCOR) NMR experiments, demonstrating that the SF and cellulose are miscible at the molecular level. Moreover, it is also found that the -NH groups of SF prefer to form hydrogen bonds with the hydroxyl groups bonded to carbons C2 and C3 of cellulose, while the hydroxyl groups bonded to carbon C6 and the ether oxygen are less favorable for hydrogen bonding interactions with the -NH groups of SF. Interestingly, bound water is found to be present in the air-dried cellulose/SF blend film, which is predominantly associated with the cellulose backbones as determined by 2D 1 H- 13 C wide-line-separation (WISE) experiments with spin diffusion. This clearly reveals the presence of nanoheterogeneity in the cellulose/SF blend film, although cellulose and SF are miscible at a molecular level. Without doubt

  19. Organophotocatalysis: Insights into the Mechanistic Aspects of Thiourea-Mediated Intermolecular [2+2] Photocycloadditions.

    Science.gov (United States)

    Vallavoju, Nandini; Selvakumar, Sermadurai; Pemberton, Barry C; Jockusch, Steffen; Sibi, Mukund P; Sivaguru, Jayaraman

    2016-04-25

    Mechanistic investigations of the intermolecular [2+2] photocycloaddition of coumarin with tetramethylethylene mediated by thiourea catalysts reveal that the reaction is enabled by a combination of minimized aggregation, enhanced intersystem crossing, and altered excited-state lifetime(s). These results clarify how the excited-state reactivity can be manipulated through catalyst-substrate interactions and reveal a third mechanistic pathway for thiourea-mediated organo-photocatalysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-09

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

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

    Directory of Open Access Journals (Sweden)

    Alexander S. Mikherdov

    2018-02-01

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

  3. Determination of intermolecular transfer integrals from DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-01

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

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

    International Nuclear Information System (INIS)

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

    1994-01-01

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

  5. Importance of the Donor:Fullerene intermolecular arrangement for high-efficiency organic photovoltaics

    KAUST Repository

    Graham, Kenneth; Cabanetos, Clement; Jahnke, Justin P.; Idso, Matthew N.; El Labban, Abdulrahman; Ngongang Ndjawa, Guy Olivier; Heumueller, Thomas; Vandewal, Koen; Salleo, Alberto; Chmelka, Bradley F.; Amassian, Aram; Beaujuge, Pierre; McGehee, Michael D.

    2014-01-01

    The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b]dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) 13C{1H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems

  6. Importance of the Donor:Fullerene intermolecular arrangement for high-efficiency organic photovoltaics

    KAUST Repository

    Graham, Kenneth

    2014-07-09

    The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b]dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) 13C{1H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems

  7. Optimizing Noncovalent Interactions Between Lignin and Synthetic Polymers to Develop Effective Compatibilizers

    Energy Technology Data Exchange (ETDEWEB)

    Henry, Nathan [University of Tennessee, Knoxville (UTK); Harper, David [University of Tennessee, Knoxville (UTK), Center for Renewable Carbon; Dadmun, Mark D [ORNL

    2012-01-01

    Experiments are designed and completed to identify an effective polymeric compatibilizer for lignin polystyrene blends. Copolymers of styrene and vinylphenol are chosen as the structure of the compatibilizer as the VPh unit can readily form intermolecular hydrogen bonds with the lignin molecule. Electron microscopy, thermal analysis, and neutron refl ectivity results demonstrate that among these compatibilizers, a copolymer of styrene and VPh with 20% 30% VPh most readily forms intermolecular interactions with the lignin molecule and results in the most well-dispersed blends with lignin. This behavior is explained by invoking the competition of intra- and intermolecular hydrogen bonding and functional group accessibility in forming intermolecular interactions.

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

    Directory of Open Access Journals (Sweden)

    Hernan Garcia-Ruiz

    2018-03-01

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

  9. Enhanced fullerene–Au(111 coupling in (2√3 × 2√3R30° superstructures with intermolecular interactions

    Directory of Open Access Journals (Sweden)

    Michael Paßens

    2015-06-01

    Full Text Available Disordered and uniform (2√3 × 2√3R30° superstructures of fullerenes on the Au(111 surface have been studied using scanning tunneling microscopy and spectroscopy. It is shown that the deposition and growth process of a fullerene monolayer on the Au(111 surface determine the resulting superstructure. The supply of thermal energy is of importance for the activation of a Au vacancy forming process and thus, one criterion for the selection of the respective superstructure. However, here it is depicted that a vacancy–adatom pair can be formed even at room temperature. This latter process results in C60 molecules that appear slightly more bright in scanning tunnelling microscopy images and are identified in disordered (2√3 x 2√3R30° superstructures based on a detailed structure analysis. In addition, these slightly more bright C60 molecules form uniform (2√3 x 2√3R30° superstructures, which exhibit intermolecular interactions, likely mediated by Au adatoms. Thus, vacancy–adatom pairs forming at room temperature directly affect the resulting C60 superstructure. Differential conductivity spectra reveal a lifting of the degeneracy of the LUMO and LUMO+1 orbitals in the uniform (2√3 x 2√3R30° superstructure and in addition, hybrid fullerene–Au(111 surface states suggest partly covalent interactions.

  10. Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions.

    Science.gov (United States)

    Wen, Jin; Li, Wei; Chen, Shuang; Ma, Jing

    2016-08-17

    Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.

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

    Science.gov (United States)

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

    2014-12-11

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

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

    Science.gov (United States)

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

    2014-12-14

    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.

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

    Directory of Open Access Journals (Sweden)

    Ming Xu

    2007-02-01

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

  14. On the importance and origin of aromatic interactions in chemistry and biodisciplines

    Czech Academy of Sciences Publication Activity Database

    Riley, Kevin Eugene; Hobza, Pavel

    2013-01-01

    Roč. 46, č. 4 (2013), s. 927-936 ISSN 0001-4842 R&D Projects: GA ČR GBP208/12/G016 Grant - others:Operational Program Research and Development for Innovations(XE) CZ.1.05/2.1.00/03.0058 Institutional support: RVO:61388963 Keywords : pi-pi interactions * potential-energy surface * ab-initio calculation * benzene dimer * intermolecular interaction * protein rubredoxin Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 24.348, year: 2013

  15. Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping--a novel approach to assess intermolecular protein contacts

    DEFF Research Database (Denmark)

    Bennett, K L; Kussmann, M; Björk, P

    2000-01-01

    The intermolecular contact regions between monomers of the homodimeric DNA binding protein ParR and the interaction between the glycoproteins CD28 and CD80 were investigated using a strategy that combined chemical cross-linking with differential MALDI-MS analyses. ParR dimers were modified in vit...

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

    Directory of Open Access Journals (Sweden)

    Phannika Kanthima

    2016-01-01

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

  17. Electron correlation effects on the N2--N2 interaction

    International Nuclear Information System (INIS)

    Hay, P.J.; Pack, R.T.; Martin, R.L.

    1984-01-01

    Ab initio self-consistent field, configuration interaction, and many-body perturbation theory methods are used to calculate the intermolecular potential between two nitrogen molecules. The emphasis is placed on the repulsive region important at the temperatures and pressures encountered in detonations. In addition, electron gas calculations are employed to fit and extend the ab initio data. We also generate effective spherical potentials which fit dilute gas virial, viscosity, and differential scattering data while being constrained by Hugoniot or ab initio data in the repulsive region. Finally, we discuss the roles of electron correlation and of many-body effects on the N 2 --N 2 interaction. Comparisons are also made to the Ar 2 potential where similar ab initio calculations are compared to an accurate empirical potential

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Roncaratti, L. F., E-mail: lz@fis.unb.br; Leal, L. A.; Silva, G. M. de [Instituto de Física, Universidade de Brasília, 70910 Brasília (Brazil); Pirani, F. [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Aquilanti, V. [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Instituto de Física, Universidade Federal da Bahia, 40210 Salvador (Brazil); Gargano, R. [Instituto de Física, Universidade de Brasília, 70910 Brasília (Brazil); Departments of Chemistry and Physics, University of Florida, Quantum Theory Project, Gainesville, Florida 32611 (United States)

    2014-10-07

    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 H{sub 2}O{sub 2}−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 H{sub 2}O{sub 2} molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H{sub 2}O{sub 2} 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.

  20. Effect of secondary structure on the interactions of peptide T4 LYS (11-36) in mixtures of aqueous sodium chloride and 2,2,2,-Trifluoroethanol

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Camille O.; Spiegelberg, Susanne; Prausnitz, John M.; Blanch, Harvey W.

    2001-10-01

    The potential of mean force for protein-protein interactions is key to the development of a statistical-mechanical model for salt-induced protein precipitation and crystallization, and for understanding certain disease states, including cataract formation and {beta}-amyloid pathology in Alzheimer's disease. Fluorescence anisotropy provides a method for quantitative characterization of intermolecular interactions due to reversible association. Monomer-dimer equilibria for the peptide T4 LYS(11-36) were studied by fluorescence anisotropy. This peptide, derived from the {beta}-sheet region of the T4 lysozyme molecule, has the potential to form amyloid fibrils. 2,2,2-trifluoroethanol (TFE) induces a change in peptide secondary structure, and was used in aqueous solutions at concentrations from 0 to 50% (v/v) at 25 and 37 C to examine the role of peptide conformation on peptide-peptide interactions. The association constant for dimerization increased with rising TFE concentration and with falling temperature. The peptide-peptide potential of mean force was computed from these association constants. Circular-dichroism measurements showed that the secondary structure of the peptide plays an important role in these strong attractive interactions due to intermolecular hydrogen-bond formation and hydrophobic interactions.

  1. Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO.

    Directory of Open Access Journals (Sweden)

    Marcos Rodrigo Alborghetti

    Full Text Available Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans, SCOCO (short coiled-coil protein / UNC-69 and kinesins (e.g. kinesin heavy chain / UNC116 are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth, we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance, cross-linking coupled with mass spectrometry (MS, SAXS (Small Angle X-ray Scattering and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance studies of the region involved in this process, corresponding to FEZ1 (92-194. Through studies involving the protein in its monomeric configuration (reduced and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.

  2. Multi-property isotropic intermolecular potentials and predicted spectral lineshapes of collision-induced absorption (CIA), collision-induced light scattering (CILS) and collision-induced hyper-Rayleigh scattering (CIHR) for H2sbnd Ne, -Kr and -Xe

    Science.gov (United States)

    El-Kader, M. S. A.; Godet, J.-L.; Gustafsson, M.; Maroulis, G.

    2018-04-01

    Quantum mechanical lineshapes of collision-induced absorption (CIA), collision-induced light scattering (CILS) and collision-induced hyper-Rayleigh scattering (CIHR) at room temperature (295 K) are computed for gaseous mixtures of molecular hydrogen with neon, krypton and xenon. The induced spectra are detected using theoretical values for induced dipole moment, pair-polarizability trace and anisotropy, hyper-polarizability and updated intermolecular potentials. Good agreement is observed for all spectra when the literature and the present potentials which are constructed from the transport and thermo-physical properties are used.

  3. The experimental charge-density approach in the evaluation of intermolecular interactions. Application of a new module of the XD programming package to several solids including a pentapeptide.

    Science.gov (United States)

    Abramov, Y A; Volkov, A; Wu, G; Coppens, P

    2000-11-01

    A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, L-asparagine monohydrate and the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol). The electrostatic interactions are evaluated with the atom-centered distributed multipoles from KRMM (kappa'-restricted multipole model) refinements, using the Buckingham expression for non-overlapping charge densities. Results for p-nitroaniline are compared with Hartree-Fock (HF), density functional (DFT) and Moller-Plesset (MP2) supermolecular calculations and with HF and DFT periodic calculations. The HF and DFT methods fail to predict the stability of the p-nitroaniline crystal but the results of the experimental charge-density approach (ECDA) are in good agreement with both MP2 interaction energies and the experimental lattice energy. ECDA results for L-asparagine monohydrate compare well with those from DFT supermolecular and periodic HF calculations. The disorder of the terminal group in the pentapeptide, which persists at the experimental temperature of 20 K, corresponds to an energy difference of only 0.35 kJ mol(-1), which is too small to be reproduced with current methods.

  4. Cohesion: a scientific history of intermolecular forces

    National Research Council Canada - National Science Library

    Rowlinson, J. S

    2002-01-01

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

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

    Science.gov (United States)

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

    2018-04-01

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

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

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  7. Investigating Molecular Interactions

    DEFF Research Database (Denmark)

    Clausen, Henrik Fanø

    2010-01-01

    ···π interactions are accommodated by electrostatic complementarity. The crystal structure of both the α- and the β-polymorph of hydroquinone is presented in Chapter 6 with focus on close intermolecular contacts between the molecules via Hirshfeld surface analysis. The charge density distribution of the empty β....... The last chapter of this dissertation presents the analysis of intermolecular interaction using both the Hirshfeld surface and charge density distribution of the acetonitrile β-hydroquinone clathrate. The local packing and related close contacts are examined by breakdown of the fingerprint plots revealing......, are also introduced, as a goal of the analysis of charge density distributions is to obtain further understanding of these macroscopic properties. Neutron diffraction will be used as a complementary tool to the X-ray diffraction experiment, as positional and thermal parameters of hydrogen atoms can...

  8. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    Science.gov (United States)

    Mundell, Donald W.

    2007-01-01

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

  9. Diatomic interaction potential theory applications

    CERN Document Server

    Goodisman, Jerry

    2013-01-01

    Diatomic Interaction Potential Theory, Volume 2: Applications discusses the variety of applicable theoretical material and approaches in the calculations for diatomic systems in their ground states. The volume covers the descriptions and illustrations of modern calculations. Chapter I discusses the calculation of the interaction potential for large and small values of the internuclear distance R (separated and united atom limits). Chapter II covers the methods used for intermediate values of R, which in principle means any values of R. The Hartree-Fock and configuration interaction schemes des

  10. Phase transitions in liquids with directed intermolecular bonding

    OpenAIRE

    Son, L.; Ryltcev, R.

    2005-01-01

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

  11. Digital communication through intermolecular fluorescence modulation.

    Science.gov (United States)

    Raymo, F M; Giordani, S

    2001-06-14

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

  12. Studies on electrospun nylon-6/chitosan complex nanofiber interactions

    International Nuclear Information System (INIS)

    Zhang Haitao; Li Shubai; Branford White, Christopher J.; Ning Xin; Nie Huali; Zhu Limin

    2009-01-01

    Composite membranes of nylon-6/chitosan nanofibers with different weight ratio of nylon-6 to chitosan were fabricated successfully using electrospinning. Morphologies of the nanofibers were investigated by scanning electron microscopy (SEM) and the intermolecular interactions of the nylon-6/chitosan complex were evaluated by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), differential scanning calorimetry (DSC) as well as mechanical testing. We found that morphology and diameter of the nanofibers were influenced by the concentration of the solution and weight ratio of the blending component materials. Furthermore FT-IR analyses on interactions between components demonstrated an IR band frequency shift that appeared to be dependent on the amount of chitosan in the complex. Observations from XRD and DSC suggested that a new fraction of γ phase crystals appeared and increased with the increasing content of chitosan in blends, this indicated that intermolecular interactions occurred between nylon-6 and chitosan. Results from performance data in mechanical showed that intermolecular interactions varied with varying chitosan content in the fibers. It was concluded that a new composite product was created and the stability of this system was attributed to strong new interactions such as hydrogen bond formation between the nylon-6 polymers and chitosan structures.

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

    Science.gov (United States)

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2013-09-01

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

  14. Opalescence in monoclonal antibody solutions and its correlation with intermolecular interactions in dilute and concentrated solutions.

    Science.gov (United States)

    Raut, Ashlesha S; Kalonia, Devendra S

    2015-04-01

    Opalescence indicates physical instability of a formulation because of the presence of aggregates or liquid-liquid phase separation in solution and has been reported for monoclonal antibody (mAb) formulations. Increased solution opalescence can be attributed to attractive protein-protein interactions (PPIs). Techniques including light scattering, AUC, or membrane osmometry are routinely employed to measure PPIs in dilute solutions, whereas opalescence is seen at relatively higher concentrations, where both long- and short-range forces contribute to overall PPIs. The mAb molecule studied here shows a unique property of high opalescence because of liquid-liquid phase separation. In this study, opalescence measurements are correlated to PPIs measured in diluted and concentrated solutions using light scattering (kD ) and high-frequency rheology (G'), respectively. Charges on the molecules were calculated using zeta potential measurements. Results indicate that high opalescence and phase separation are a result of the attractive interactions in solution; however, the presence of attractive interactions do not always imply phase separation. Temperature dependence of opalescence suggests that thermodynamic contribution to opalescence is significant and Tcloud can be utilized as a potential tool to assess attractive interactions in solution. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  15. Useful lower limits to polarization contributions to intermolecular interactions using a minimal basis of localized orthogonal orbitals: theory and analysis of the water dimer.

    Science.gov (United States)

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

    2013-02-28

    The problem of describing the energy-lowering associated with polarization of interacting molecules is considered in the overlapping regime for self-consistent field wavefunctions. The existing approach of solving for absolutely localized molecular orbital (ALMO) coefficients that are block-diagonal in the fragments is shown based on formal grounds and practical calculations to often overestimate the strength of polarization effects. A new approach using a minimal basis of polarized orthogonal local MOs (polMOs) is developed as an alternative. The polMO basis is minimal in the sense that one polarization function is provided for each unpolarized orbital that is occupied; such an approach is exact in second-order perturbation theory. Based on formal grounds and practical calculations, the polMO approach is shown to underestimate the strength of polarization effects. In contrast to the ALMO method, however, the polMO approach yields results that are very stable to improvements in the underlying AO basis expansion. Combining the ALMO and polMO approaches allows an estimate of the range of energy-lowering due to polarization. Extensive numerical calculations on the water dimer using a large range of basis sets with Hartree-Fock theory and a variety of different density functionals illustrate the key considerations. Results are also presented for the polarization-dominated Na(+)CH4 complex. Implications for energy decomposition analysis of intermolecular interactions are discussed.

  16. Calculation of Rydberg interaction potentials

    International Nuclear Information System (INIS)

    Weber, Sebastian; Büchler, Hans Peter; Tresp, Christoph; Urvoy, Alban; Hofferberth, Sebastian; Menke, Henri; Firstenberg, Ofer

    2017-01-01

    The strong interaction between individual Rydberg atoms provides a powerful tool exploited in an ever-growing range of applications in quantum information science, quantum simulation and ultracold chemistry. One hallmark of the Rydberg interaction is that both its strength and angular dependence can be fine-tuned with great flexibility by choosing appropriate Rydberg states and applying external electric and magnetic fields. More and more experiments are probing this interaction at short atomic distances or with such high precision that perturbative calculations as well as restrictions to the leading dipole–dipole interaction term are no longer sufficient. In this tutorial, we review all relevant aspects of the full calculation of Rydberg interaction potentials. We discuss the derivation of the interaction Hamiltonian from the electrostatic multipole expansion, numerical and analytical methods for calculating the required electric multipole moments and the inclusion of electromagnetic fields with arbitrary direction. We focus specifically on symmetry arguments and selection rules, which greatly reduce the size of the Hamiltonian matrix, enabling the direct diagonalization of the Hamiltonian up to higher multipole orders on a desktop computer. Finally, we present example calculations showing the relevance of the full interaction calculation to current experiments. Our software for calculating Rydberg potentials including all features discussed in this tutorial is available as open source. (tutorial)

  17. In vivo interactions between the proteins of infectious bursal disease virus: capsid protein VP3 interacts with the RNA dependent polymerase VP1

    NARCIS (Netherlands)

    Tacken, M.G.J.; Rottier, P.J.M.; Gielkens, A.L.J.; Peeters, B.P.H.

    2000-01-01

    Little is known about the intermolecular interactions between the viral proteins of infectious bursal disease virus (IBDV). By using the yeast two-hybrid system, which allows the detection of protein-protein interactions in vivo, all possible interactions were tested by fusing the viral proteins to

  18. Interactions in vivo between the proteins of infectious bursal disease virus: capsid protein VP3 interacts with the RNA-dependent polymerase, VP1

    NARCIS (Netherlands)

    Tacken, M.G.J.; Rottier, P.J.M.; Gielkens, A.L.J.; Peeters, B.P.H.

    2000-01-01

    Little is known about the intermolecular interactions between the viral proteins of infectious bursal disease virus (IBDV). By using the yeast two-hybrid system, which allows the detection of protein-protein interactions in vivo, all possible interactions were tested by fusing the viral proteins to

  19. Molecular electrostatics for probing lone pair-π interactions.

    Science.gov (United States)

    Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

    2013-11-14

    An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

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

    Science.gov (United States)

    Li, An Yong

    2007-04-21

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

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

    Directory of Open Access Journals (Sweden)

    Jungho Jun

    2013-08-01

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

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

    International Nuclear Information System (INIS)

    Jee, Jun Goo

    2010-01-01

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

  3. Molecular Understanding of Fullerene - Electron Donor Interactions in Organic Solar Cells

    KAUST Repository

    Ryno, Sean

    2016-09-13

    Organic solar cells hold promise of providing low-cost, renewable power generation, with current devices providing up to 13% power conversion efficiency. The rational design of more performant systems requires an in-depth understanding of the interactions between the electron donating and electron accepting materials within the active layers of these devices. Here, we explore works that give insight into the intermolecular interactions between electron donors and electron acceptors, and the impact of molecular orientations and environment on these interactions. We highlight, from a theoretical standpoint, the effects of intermolecular interactions on the stability of charge carriers at the donor/acceptor interface and in the bulk and how these interactions influence the nature of the charge transfer states as wells as the charge separation and charge transport processes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    Wang, Hui; Liu, Ju; Wang, Weizhou

    2018-02-14

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

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

    Science.gov (United States)

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2014-06-01

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

  6. Photoinduced intermolecular electron transfer and off-resonance Raman characteristics of Rhodamine 101/N,N-diethylaniline

    International Nuclear Information System (INIS)

    Jiang, Li-lin; Liu, Wei-long; Song, Yun-fei; He, Xing; Wang, Yang; Wang, Chang; Wu, Hong-lin; Yang, Fang; Yang, Yan-qiang

    2014-01-01

    Highlights: • Mechanism of PIET reaction process for the Rh101 + /DEA system is investigated. • The significant geometrical changes of the charge–transfer complex are explained. • Forward Electron transfer from DEA to Rh101 +∗ occurs with lifetime of 425–560 fs. • Backward electron transfer occurs with a time constant of 46.16–51.40 ps. • Intramolecular vibrational relaxation occurs with lifetime of 2.77–5.39 ps. - Abstract: The ultrafast photoinduced intermolecular electron transfer (PIET) reaction of Rhodamine 101 (Rh101 + ) in N,N-diethylaniline (DEA) was investigated using off-resonance Raman, femtosecond time-resolved multiplex transient grating (TG) and transient absorption (TA) spectroscopies. The Raman spectra indicate that the C=C stretching vibration of the chromophore aromatic ring is more sensitive to ET compared with the C-C stretching mode. The ultrafast photoinduced intermolecular forward ET (FET) from DEA to Rh101 +∗ occurs on a time scale of τ FET = 425–560 fs. The backward ET (BET) occurs in the inverted region with a time constant of τ BET = 46.16–51.40 ps. The intramolecular vibrational relaxation (IVR) process occurs on the excited state potential energy surface with the time constant of τ IVR = 2.77–5.39 ps

  7. Hyperspherical effective interaction for nonlocal potentials

    International Nuclear Information System (INIS)

    Barnea, N.; Leidemann, W.; Orlandini, G.

    2010-01-01

    The effective interaction hyperspherical-harmonics method, formulated for local forces, is generalized to accommodate nonlocal interactions. As for local potentials this formulation retains the separation of the hyper-radial part leading solely to a hyperspherical effective interaction. By applying the method to study ground-state properties of 4 He with a modern effective-field-theory nucleon-nucleon potential model (Idaho-N3LO), one finds a substantial acceleration in the convergence rate of the hyperspherical-harmonics series. Also studied are the binding energies of the six-body nuclei 6 He and 6 Li with the JISP16 nuclear force. Again an excellent convergence is observed.

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

    International Nuclear Information System (INIS)

    Fries, P.

    1978-01-01

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

  9. Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments.

    Science.gov (United States)

    Dubinets, Nikita; Slipchenko, Lyudmila V

    2017-07-20

    Accuracy of the effective fragment potential (EFP) method was explored for describing intermolecular interaction energies in three dimers with strong H-bonded interactions, formic acid, formamide, and formamidine dimers, which are a part of HBC6 database of noncovalent interactions. Monomer geometries in these dimers change significantly as a function of intermonomer separation. Several EFP schemes were considered, in which fragment parameters were prepared for a fragment in its gas-phase geometry or recomputed for each unique fragment geometry. Additionally, a scheme in which gas-phase fragment parameters are shifted according to relaxed fragment geometries is introduced and tested. EFP data are compared against the coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) method in a complete basis set (CBS) and the symmetry adapted perturbation theory (SAPT). All considered EFP schemes provide a good agreement with CCSD(T)/CBS for binding energies at equilibrium separations, with discrepancies not exceeding 2 kcal/mol. However, only the schemes that utilize relaxed fragment geometries remain qualitatively correct at shorter than equilibrium intermolecular distances. The EFP scheme with shifted parameters behaves quantitatively similar to the scheme in which parameters are recomputed for each monomer geometry and thus is recommended as a computationally efficient approach for large-scale EFP simulations of flexible systems.

  10. Separable expansions for local potentials with Coulomb interactions

    International Nuclear Information System (INIS)

    Adhikari, S.K.

    1976-01-01

    If two particles are interacting via a short range potential and a repulsive Coulomb potential the t matrix can be written as a sum of the Coulomb and the ''nuclear'' t matrices. In order to solve the three-nucleon problem with Coulomb interactions usually we need a separable representation of this ''nuclear'' t matrix. A recently proposed method for finding a separable expansion for local potentials is here extended to find a rapidly convergent separable expansion, with analytic form factors, for the ''nuclear'' part of the t matrix of a local potential, in the presence of Coulomb interactions. The method is illustrated for a two-term Malfliet-Tjon potential. In each rank the ''nuclear'' phase shift is close to the corresponding phase shift when the Coulomb interaction is switched off

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

    Science.gov (United States)

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

    2007-11-01

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

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

    Science.gov (United States)

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

    2011-08-01

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

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

    Science.gov (United States)

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

    2006-08-01

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

  14. On singular interaction potentials in classical statistical mechanics

    International Nuclear Information System (INIS)

    Zagrebnov, V.A.; Pastur, L.A.

    1978-01-01

    A classical system of particles with stable two-body interaction potential is considered. It is shown that for a certain class of highly singular stable two-body potentials a cut-off procedure preserves the stability of the potential. The thermodynamical potentials (pressure and free energy density) and correlation functions are proved to have the property of asymptotic independence with respect to the continuation of the interaction potentials near singularity

  15. Ligand-receptor Interactions by NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Novak. P.

    2008-04-01

    Full Text Available Today NMR spectroscopy is a method of choice for elucidation of interactions between biomolecules and the potential ligands. Knowledge on these interactions is an essential prerequisite for the rational drug design. The most important contribution of NMR to drug design a few years ago was the 3D structure determination of proteins. Besides delivering the 3D structures of the free proteins as a raw material for the modeling studies on ligand binding, NMR can directly yield valuable experimental data on the biologically important protein-ligand complexes. In addition to X-ray diffraction, NMR spectroscopy can provide information on the internal protein dynamics ordynamics of intermolecular interactions. Changes in NMR parameters allow us to detect ("SAR by NMR" and quantitatively determine binding affinities (titration, diffusion NMR experiments, etc. of potential ligands. Also, it is possible to determine the binding site and conformations of ligands, receptors and receptor-ligand complexes with the help of NMR methods such as tr-NOESY. Epitopes or functional groups responsible for binding of ligands to the receptor can be identified by employing STD or WaterLOGSY experiments. In this review are described some of the most frequent NMR methods for the characterization of the interactions between biomolecules and ligands, together with their advantages and disadvantages.

  16. Intermolecular G-quadruplex structure-based fluorescent DNA detection system.

    Science.gov (United States)

    Zhou, Hui; Wu, Zai-Sheng; Shen, Guo-Li; Yu, Ru-Qin

    2013-03-15

    Adopting multi-donors to pair with one acceptor could improve the performance of fluorogenic detection probes. However, common dyes (e.g., fluorescein) in close proximity to each other would self-quench the fluorescence, and the fluorescence is difficult to restore. In this contribution, we constructed a novel "multi-donors-to-one acceptor" fluorescent DNA detection system by means of the intermolecular G-quadruplex (IGQ) structure-based fluorescence signal enhancement combined with the hairpin oligonucleotide. The novel IGQ-hairpin system was characterized using the p53 gene as the model target DNA. The proposed system showed an improved assay performance due to the introduction of IGQ-structure into fluorescent signaling probes, which could inhibit the background fluorescence and increase fluorescence restoration amplitude of fluoresceins upon target DNA hybridization. The proof-of-concept scheme is expected to provide new insight into the potential of G-quadruplex structure and promote the application of fluorescent oligonucleotide probes in fundamental research, diagnosis, and treatment of genetic diseases. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Asymmetric Response toward Molecular Fluorination in Binary Copper–Phthalocyanine/Pentacene Assemblies

    DEFF Research Database (Denmark)

    de Oteyza, D. G.; García Lastra, Juan Maria; Goiri, E.

    2014-01-01

    We report a didactic and simple example of the subtleness in the balance of intermolecular and molecule–substrate interactions and its effect on molecular self-assembly. The study is performed on two closely related molecular blends of copper phthalocyanines and pentacene, in each of which one of...... intermolecular interactions and a larger corrugation in the molecule–substrate interaction potential, results in a disordered layer. However, the difference between the two blend’s structures vanishes when substrates with less corrugated interaction potentials are used....

  18. Nanoparticles in ionic liquids: interactions and organization.

    Science.gov (United States)

    He, Zhiqi; Alexandridis, Paschalis

    2015-07-28

    Ionic liquids (ILs), defined as low-melting organic salts, are a novel class of compounds with unique properties and a combinatorially great chemical diversity. Ionic liquids are utilized as synthesis and dispersion media for nanoparticles as well as for surface functionalization. Ionic liquid and nanoparticle hybrid systems are governed by a combined effect of several intermolecular interactions between their constituents. For each interaction, including van der Waals, electrostatic, structural, solvophobic, steric, and hydrogen bonding, the characterization and quantitative calculation methods together with factors affecting these interactions are reviewed here. Various self-organized structures based on nanoparticles in ionic liquids are generated as a result of a balance of these intermolecular interactions. These structures, including colloidal glasses and gels, lyotropic liquid crystals, nanoparticle-stabilized ionic liquid-containing emulsions, ionic liquid surface-functionalized nanoparticles, and nanoscale ionic materials, possess properties of both ionic liquids and nanoparticles, which render them useful as novel materials especially in electrochemical and catalysis applications. This review of the interactions within nanoparticle dispersions in ionic liquids and of the structure of nanoparticle and ionic liquid hybrids provides guidance on the rational design of novel ionic liquid-based materials, enabling applications in broad areas.

  19. Theoretical studies of molecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Lester, W.A. Jr. [Univ. of California, Berkeley (United States)

    1993-12-01

    This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

  20. Heteroleptic and Homoleptic Iron(III Spin-Crossover Complexes; Effects of Ligand Substituents and Intermolecular Interactions between Co-Cation/Anion and the Complex

    Directory of Open Access Journals (Sweden)

    Wasinee Phonsri

    2017-08-01

    Full Text Available The structural and magnetic properties of a range of new iron(III bis-tridentate Schiff base complexes are described with emphasis on how intermolecular structural interactions influence spin states and spin crossover (SCO in these d5 materials. Three pairs of complexes were investigated. The first pair are the neutral, heteroleptic complexes [Fe(3-OMe-SalEen(thsa] 1 and [Fe(3-MeOSalEen(3-EtOthsa] 2, where 3-R-HSalEen = (E-2-(((2-(ethylaminoethyliminomethyl-6-R-phenol and 3-R-H2thsa = thiosemicarbazone-3-R-salicylaldimine. They display spin transitions above room temperature. However, 2 shows incomplete and gradual change, while SCO in 1 is complete and more abrupt. Lower cooperativity in 2 is ascribed to the lack of π–π interactions, compared to 1. The second pair, cationic species [Fe(3-EtOSalEen2]NO3 3 and [Fe(3-EtOSalEen2]Cl 4 differ only in the counter-anion. They show partial SCO above room temperature with 3 displaying a sharp transition at 343 K. Weak hydrogen bonds from cation to Cl− probably lead to weaker cooperativity in 4. The last pair, CsH2O[Fe(3-MeO-thsa2] 5 and Cs(H2O2[Fe(5-NO2-thsa2] 6, are anionic homoleptic chelates that have different substituents on the salicylaldiminate rings of thsa2−. The Cs cations bond to O atoms of water and the ligands, in unusual ways thus forming attractive 1D and 3D networks in 5 and 6, respectively, and 5 remains HS (high spin at all temperatures while 6 remains LS (low spin. Comparisons are made to other literature examples of Cs salts of [Fe(5-R-thsa2]− (R = H and Br.

  1. Risk factors for potential drug interactions in general practice

    DEFF Research Database (Denmark)

    Bjerrum, Lars; Gonzalez Lopez-Valcarcel, Beatriz; Petersen, Gert

    2008-01-01

    interactions during 1 year. Patient factors associated with increased risk of potential drug interactions were high age, a high number of concurrently used drugs, and a high number of prescribers. Practice factors associated with potential drug interactions were a high percentage of elderly patients and a low......Objective: To identify patient- and practice-related factors associated with potential drug interactions. Methods: A register analysis study in general practices in the county of Funen, Denmark. Prescription data were retrieved from a population-based prescription database (Odense University......, depending on the severity of outcome and the quality of documentation. A two-level random coefficient logistic regression model was used to investigate factors related to potential drug interactions. Results: One-third of the population was exposed to polypharmacy, and 6% were exposed to potential drug...

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

    KAUST Repository

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

    2017-01-01

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

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

    Science.gov (United States)

    Alkorta, Ibon; Elguero, José; Elguero, Eric

    2017-11-01

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

  4. Small angle X-ray scattering on concentrated hemoglobin solutions

    International Nuclear Information System (INIS)

    Zinke, M.; Damaschun, G.; Mueller, J.J.; Ruckpaul, K.

    1978-01-01

    The small-angle X-ray scattering technique was used to determine the intermolecular structure and interaction potentials in oxi-and deoxi-hemoglobin solutions. The pair correlation function obtained by the ZERNICKE-PRINS equation characterizes the intermolecular structure of the hemoglobin molecules. The intermolecular structure is concentration dependent. The hemoglobin molecules have a 'short range order structure' with a range of about 4 molecule diameters at 324 g/l. The potential functions of the hemoglobin-hemoglobin interaction have been determined on the basis of fluid theories. Except for the deoxi-hemoglobin solution having the concentration 370 g/l, the pair interaction consists in a short repulsion and a weak short-range attraction against kT. The potential minimum is between 1.2 - 1.5 nm above the greatest hemoglobin diameter. (author)

  5. Photoinduced intermolecular electron transfer and off-resonance Raman characteristics of Rhodamine 101/N,N-diethylaniline

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Li-lin [Department of Physics, Harbin Institute of Technology, Harbin 150001 (China); School of Mechanical and Electronic Engineering, Hezhou University, Hezhou 542800 (China); Liu, Wei-long; Song, Yun-fei; He, Xing; Wang, Yang; Wang, Chang; Wu, Hong-lin [Department of Physics, Harbin Institute of Technology, Harbin 150001 (China); Yang, Fang [National Key Laboratory of Science and Technology on Tunable Laser, Department of Optoelectronics Information Science Technology, Harbin Institute of Technology, Harbin 150001 (China); Yang, Yan-qiang, E-mail: yqyang@hit.edu.cn [Department of Physics, Harbin Institute of Technology, Harbin 150001 (China); National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, Sichuan (China)

    2014-01-31

    Highlights: • Mechanism of PIET reaction process for the Rh101{sup +}/DEA system is investigated. • The significant geometrical changes of the charge–transfer complex are explained. • Forward Electron transfer from DEA to Rh101{sup +∗} occurs with lifetime of 425–560 fs. • Backward electron transfer occurs with a time constant of 46.16–51.40 ps. • Intramolecular vibrational relaxation occurs with lifetime of 2.77–5.39 ps. - Abstract: The ultrafast photoinduced intermolecular electron transfer (PIET) reaction of Rhodamine 101 (Rh101{sup +}) in N,N-diethylaniline (DEA) was investigated using off-resonance Raman, femtosecond time-resolved multiplex transient grating (TG) and transient absorption (TA) spectroscopies. The Raman spectra indicate that the C=C stretching vibration of the chromophore aromatic ring is more sensitive to ET compared with the C-C stretching mode. The ultrafast photoinduced intermolecular forward ET (FET) from DEA to Rh101{sup +∗} occurs on a time scale of τ{sub FET} = 425–560 fs. The backward ET (BET) occurs in the inverted region with a time constant of τ{sub BET} = 46.16–51.40 ps. The intramolecular vibrational relaxation (IVR) process occurs on the excited state potential energy surface with the time constant of τ{sub IVR} = 2.77–5.39 ps.

  6. 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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-28

    We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-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 β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-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 β-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.

  7. Structure formation in bis(terpyridine) derivative adlayers: molecule-substrate versus molecule-molecule interactions.

    Science.gov (United States)

    Hoster, Harry E; Roos, Matthias; Breitruck, Achim; Meier, Christoph; Tonigold, Katrin; Waldmann, Thomas; Ziener, Ulrich; Landfester, Katharina; Behm, R Jürgen

    2007-11-06

    The influence of the substrate and the deposition conditions-vapor deposition versus deposition from solution-on the structures formed upon self-assembly of deposited bis(terpyridine) derivative (2,4'-BTP) monolayers on different hexagonal substrates, including highly oriented pyrolytic graphite (HOPG), Au(111), and (111)-oriented Ag thin films, was investigated by high-resolution scanning tunneling microscopy and by model calculations of the intermolecular energies and the lateral corrugation of the substrate-adsorbate interaction. Similar quasi-quadratic network structures with almost the same lattice constants obtained on all substrates are essentially identical to the optimum configuration expected from an optimization of the adlayer structure with C-H...N-type bridging bonds as a structure-determining factor, which underlines a key role of the intermolecular interactions in adlayer order. Slight distortions from the optimum values to form commensurate adlayer structures on the metal substrates and the preferential orientation of the adlayer with respect to the substrate are attributed to the substrate-adsorbate interactions, specifically, the lateral corrugation in the substrate-adsorbate interaction upon lateral displacement and rotation of the adsorbed BTP molecules. The fact that similar adlayer structures are obtained on HOPG under ultrahigh vacuum conditions (solid|gas interface) and on HOPG in trichlorobenzene (solid|liquid interface) indicates that the intermolecular interactions are not severely affected by the solvent.

  8. Measuring Intermolecular Binding Energies by Laser Spectroscopy.

    Science.gov (United States)

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

    2017-02-22

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

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

    Science.gov (United States)

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

    2013-11-28

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

  10. Metastable He (n=2) - Ne potential interaction calculation

    International Nuclear Information System (INIS)

    Rahal, H.

    1983-10-01

    Diabatic potential terms corresponding to He (2 1 S)-Ne and He (2 3 S)-Ne interactions are calculated. These potentials reproduce the experimental results thermal metastable atom elastic scattering on Ne target. A model which reduces the interaction to a one-electron problem is proposed: the He excited electron. Its interaction with the He + center is reproduced by a ''l'' dependent potential model with a 1/2 behaviour at short range. The electron interaction facing the Ne is described by a l-dependent pseudopotential reproducing with accuracy the electron elastic scattering on a Ne atom. The importance of the corrective term related to the Ne polarizations by the electron and the He + ion is showed in this work. In the modelling problems, the accuracy cannot be better than 0.1 MeV [fr

  11. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

    KAUST Repository

    Oliva, Romina; Chermak, Edrisse; Cavallo, Luigi

    2015-01-01

    In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

  12. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

    KAUST Repository

    Oliva, Romina

    2015-07-01

    In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

  13. Highly Stereoselective Intermolecular Haloetherification and Haloesterification of Allyl Amides

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

    Houjou, Hirohiko

    2011-10-01

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

  15. Weak interaction potentials of nucleons in the Weinberg-Salam model

    International Nuclear Information System (INIS)

    Lobov, G.A.

    1979-01-01

    Weak interaction potentials of nucleons due to the nonet vector meson exchange are obtained in the Weinberg-Salam model using the vector-meson dominance. Contribution from the hadronic neutral currents to the weak interaction potential due to the charged pion exchange is obtained. The isotopic structure of the obtained potentials, that is unambiguous in the Weinberg-Salam model, is investigated. Enhancement of the nucleon weak interaction in nuclei resulting from the hadronic neutral currents is discussed. A nuclear one-particle weak interaction potential is presented that is a result of averaging of the two-particle potential over the states of the nuclear core. An approach to the nucleon weak interaction based on the quark model, is discussed. Effects of the nucleon weak interaction in the radiative capture of a thermal neutron by a proton, are considered

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

    Science.gov (United States)

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

    2011-03-01

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

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

    International Nuclear Information System (INIS)

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

    1999-01-01

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

  18. Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion

    International Nuclear Information System (INIS)

    Bereau, Tristan; Lilienfeld, O. Anatole von

    2014-01-01

    We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular interaction model from dispersion and electrostatics for more than 1300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine—intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. The mean absolute error made by the combination of static electrostatics with many-body dispersion reduces at larger distances, while it plateaus for two-body dispersion, in conflict with the common assumption that the simple 1/R 6 correction will yield proper dissociative tails. Overall, the method achieves an accuracy well within conventional molecular force fields while exhibiting a simple parametrization protocol

  19. Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de [Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany and Department of Chemistry, University of Basel, 4056 Basel (Switzerland); Lilienfeld, O. Anatole von [Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4056 Basel, Switzerland and Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2014-07-21

    We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular interaction model from dispersion and electrostatics for more than 1300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine—intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. The mean absolute error made by the combination of static electrostatics with many-body dispersion reduces at larger distances, while it plateaus for two-body dispersion, in conflict with the common assumption that the simple 1/R{sup 6} correction will yield proper dissociative tails. Overall, the method achieves an accuracy well within conventional molecular force fields while exhibiting a simple parametrization protocol.

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

    Science.gov (United States)

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

    2016-11-09

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

  1. Contribution to the study of the molecular interactions of gaseous hydrofluoric acid

    International Nuclear Information System (INIS)

    Ostorero, Jean

    1972-01-01

    The experimental study is based on measurements of gaseous viscosity coefficients and on the pure rotational spectrum of HF perturbed by F 2 at pressures up to 200 Bar. The study of viscosity is made with two apparatuses: a capillary viscometer (data on monomeric HF) and a rotating cylinder viscometer (data on mono and polymeric HF, and seven binary gaseous mixtures HF-X (X = He, Ar, N 2 , F 2 , CO 2 , ClF 3 , HCl). The experimental results are used as a criterion of validity for the different interaction models for polar gases found in the literature. The two remaining models are: 1) DANON and AMDUR; 2) MONCHICK and MASON. The viscosity data of mixtures give the values of the intermolecular parameters (ε 0 , σ 0 ) of the potential isotropic part. A semi quantum calculus improves slightly the correlation in the case of the model proposed by MONCHICK and MASON. The interpretation of the pressure viscosity data of HF gives the parameters values (e, o) for the dimer and the cyclic hexamer in the vapor phase. The vanishing of the R 0 rotation line of the HF spectrum perturbed by F 2 is qualitatively interpreted as the influence of the anisotropic part of the intermolecular potential. (author) [fr

  2. Effects on the structure of monolayer and submonolayer fluid nitrogen films by the corrugation in the holding potential of nitrogen molecules

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing

    2001-01-01

    of interactions were indicated by the comparison of the calculated and measured isosteric heats of adsorption in fluid films of nitrogen molecules on graphite. The melting temperatures were lowered by 7K and a region of liquid-gas coexistence was observed for films on the smooth graphite surface indicating......The effects of corrugation in the holding potential of nitrogen molecules on the structure of fluid monolayer and submonolayer films of the molecules on a solid substrate was studied using molecular dynamics simulation. Including McLachlan mediation of the intermolecular potential in a model...

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

    Science.gov (United States)

    Meng, Qingxi; Shen, Wei; Li, Ming

    2012-03-01

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

  4. The interaction between theory and experiment in charge density analysis

    International Nuclear Information System (INIS)

    Coppens, Phillip

    2013-01-01

    The field of x-ray charge density analysis has gradually morphed into an area benefiting from the strong interactions between theoreticians and experimentalists, leading to new concepts on chemical bonding and of intermolecular interactions in condensed phases. Some highlights of the developments culminating in the 2013 Aminoff Award are described in this paper. (comment)

  5. Robust singlet fission in pentacene thin films with tuned charge transfer interactions.

    Science.gov (United States)

    Broch, K; Dieterle, J; Branchi, F; Hestand, N J; Olivier, Y; Tamura, H; Cruz, C; Nichols, V M; Hinderhofer, A; Beljonne, D; Spano, F C; Cerullo, G; Bardeen, C J; Schreiber, F

    2018-03-05

    Singlet fission, the spin-allowed photophysical process converting an excited singlet state into two triplet states, has attracted significant attention for device applications. Research so far has focused mainly on the understanding of singlet fission in pure materials, yet blends offer the promise of a controlled tuning of intermolecular interactions, impacting singlet fission efficiencies. Here we report a study of singlet fission in mixtures of pentacene with weakly interacting spacer molecules. Comparison of experimentally determined stationary optical properties and theoretical calculations indicates a reduction of charge-transfer interactions between pentacene molecules with increasing spacer molecule fraction. Theory predicts that the reduced interactions slow down singlet fission in these blends, but surprisingly we find that singlet fission occurs on a timescale comparable to that in pure crystalline pentacene. We explain the observed robustness of singlet fission in such mixed films by a mechanism of exciton diffusion to hot spots with closer intermolecular spacings.

  6. Ion mobilities and ion-atom interaction potentials

    International Nuclear Information System (INIS)

    Gatland, I.R.

    1982-01-01

    The techniques for measuring the mobilities of ions in gases, relating interaction potentials to mobilities, and determining potentials from experimental mobilities are reviewed. Applications are presented for positive alkali ions and negative halogen ions in inert gases. (Auth.)

  7. Vibrational spectroscopy on intermolecular interactions in solutions and at interfaces

    NARCIS (Netherlands)

    Nissink, Johannes Wilhelmus Maria

    1999-01-01

    In recent years, considerable progress has been made in the areas of molecular recognition and surface analysis. These fields meet in the field of sensor development, where the interaction between molecules and a suitably modified surface is of utmost importance. Vibrational spectroscopy is quite

  8. Potential intravenous drug interactions in intensive care

    Directory of Open Access Journals (Sweden)

    Maiara Benevides Moreira

    Full Text Available Abstract OBJECTIVE To analyze potential intravenous drug interactions, and their level of severity associated with the administration of these drugs based on the prescriptions of an intensive care unit. METHOD Quantitative study, with aretrospective exploratory design, and descriptive statistical analysis of the ICU prescriptions of a teaching hospital from March to June 2014. RESULTS The sample consisted of 319 prescriptions and subsamples of 50 prescriptions. The mean number of drugs per patient was 9.3 records, and a higher probability of drug interaction inherent to polypharmacy was evidenced. The study identified severe drug interactions, such as concomitant administration of Tramadol with selective serotonin reuptake inhibitor drugs (e.g., Metoclopramide and Fluconazole, increasing the risk of seizures due to their epileptogenic actions, as well as the simultaneous use of Ranitidine-Fentanyl®, which can lead to respiratory depression. CONCLUSION A previous mapping of prescriptions enables the characterization of the drug therapy, contributing to prevent potential drug interactions and their clinical consequences.

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2010-05-07

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

  11. Localization of weakly interacting Bose gas in quasiperiodic potential

    International Nuclear Information System (INIS)

    Ray, Sayak; Pandey, Mohit; Ghosh, Anandamohan; Sinha, Subhasis

    2016-01-01

    We study the localization properties of weakly interacting Bose gas in a quasiperiodic potential. The Hamiltonian of the non-interacting system reduces to the well known ‘Aubry–André model’, which shows the localization transition at a critical strength of the potential. In the presence of repulsive interaction we observe multi-site localization and obtain a phase diagram of the dilute Bose gas by computing the superfluid fraction and the inverse participation ratio. We construct a low-dimensional classical Hamiltonian map and show that the onset of localization is manifested by the chaotic phase space dynamics. The level spacing statistics also identify the transition to localized states resembling a Poisson distribution that are ubiquitous for both non-interacting and interacting systems. We also study the quantum fluctuations within the Bogoliubov approximation and compute the quasiparticle energy spectrum. Enhanced quantum fluctuation and multi-site localization phenomenon of non-condensate density are observed above the critical coupling of the potential. We briefly discuss the effect of the trapping potential on the localization of matter wave. (paper)

  12. Push it to the limit: Characterizing the convergence of common sequences of basis sets for intermolecular interactions as described by density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Witte, Jonathon [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Neaton, Jeffrey B. [Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Department of Physics, University of California, Berkeley, California 94720 (United States); Kavli Energy Nanosciences Institute at Berkeley, Berkeley, California 94720 (United States); Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2016-05-21

    With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen’s pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.

  13. Theoretical studies on the intermolecular interactions of potentially primordial base-pair analogues

    Czech Academy of Sciences Publication Activity Database

    Šponer, Judit E.; Vázquez-Mayagoitia, Á.; Sumpter, B.G.; Leszczynski, J.; Šponer, Jiří; Otyepka, M.; Banáš, P.; Fuentes-Cabrera, M.

    2010-01-01

    Roč. 16, č. 10 (2010), s. 3057-3065 ISSN 0947-6539 R&D Projects: GA MŠk(CZ) LC06030; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476 Grant - others:GA MŠk(CZ) LC512; GA AV ČR(CZ) IAA400550701; GA ČR(CZ) GD203/09/H046 Program:LC; IA; GD Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : quantum chemistry * base pairing * origin of life Subject RIV: BO - Biophysics Impact factor: 5.476, year: 2010

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

    Science.gov (United States)

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

    2010-01-01

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

  15. A Polarizable and Transferable PHAST CO 2 Potential for Materials Simulation

    KAUST Repository

    Mullen, Ashley L.; Pham, Tony; Forrest, Katherine A.; Cioce, Christian R.; McLaughlin, Keith; Space, Brian

    2013-01-01

    Reliable PHAST (Potentials with High Accuracy Speed and Transferability) intermolecular potential energy functions for CO2 have been developed from first principles for use in heterogeneous systems, including one with explicit polarization

  16. O interactions in 1,3-diphenyl-urea

    Indian Academy of Sciences (India)

    The synthesis, X-ray structure and role of intermolecular interactions have been studied in case of 1,3-diphenyl-urea, owing to its medicinal importance. The compound crystallizes in orthorhombic crystal system (space group, 21) with unit cell parameters, = 9.118(3), = 10.558(2), = 11.780(3) Å and = 4.

  17. Rhodium(III)-Catalyzed Activation of C(sp3)-H Bonds and Subsequent Intermolecular Amidation at Room Temperature.

    Science.gov (United States)

    Huang, Xiaolei; Wang, Yan; Lan, Jingbo; You, Jingsong

    2015-08-03

    Disclosed herein is a Rh(III)-catalyzed chelation-assisted activation of unreactive C(sp3)-H bonds, thus enabling an intermolecular amidation to provide a practical and step-economic route to 2-(pyridin-2-yl)ethanamine derivatives. Substrates with other N-donor groups are also compatible with the amidation. This protocol proceeds at room temperature, has a relatively broad functional-group tolerance and high selectivity, and demonstrates the potential of rhodium(III) in the promotive functionalization of unreactive C(sp3)-H bonds. A rhodacycle having a SbF6(-) counterion was identified as a plausible intermediate. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Directory of Open Access Journals (Sweden)

    Takashi Yamamoto

    2012-07-01

    Full Text Available The relationship between the conducting behavior and the degree of charge fluctuation in the β″-type BEDT-TTF salts is reviewed from the standpoints of vibrational spectroscopy and crystal structure. A group of β″-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 β″-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, ∆ρ, is a useful criterion for indicating conducting behavior. All superconductors presented in this review are characterized as small but finite ∆ρ.

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  20. Helping Students Assess the Relative Importance of Different Intermolecular Interactions

    Science.gov (United States)

    Jasien, Paul G.

    2008-01-01

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

  1. 2004 Atomic and Molecular Interactions Gordon Research Conference

    International Nuclear Information System (INIS)

    Dr. Paul J. Dagdigian

    2004-01-01

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference

  2. 2004 Atomic and Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  3. Interaction potential for two different atoms

    International Nuclear Information System (INIS)

    Kuzmichev, V.E.; Peresypkin, V.V.

    1991-01-01

    Using the rigorous approach to the nonrelativistic four Coulomb particle problem the interaction potentials between an ordinary hydrogen and muonic-hydrogen atoms at large: R>a e +a μ (1), and intermediate: a e >R>>a μ (2) distances, where a e and a μ are the Bohr radii, are calculated in the adiabatic approximation. The van der Waals potential constants in the region (1) and an explicit potential form in the region (2) taking into account both the polarization effects and the electron screening corrections are determined. 10 refs

  4. Investigation of the influence of intermolecular interactions on the electronic stopping cross sections

    International Nuclear Information System (INIS)

    Krotz, R.; Neuwirth, W.; Pietsch, W.

    1980-01-01

    The electronic stopping cross sections for Li projectiles have been measured in various kinds of targets. They are analyzed here with respect to the different types of interactions between the constituents of the target: interactions between the atoms in a compound (chemical bonding), the ion-dipole interaction, if the target is an electrolytic solution, and the dipole-dipole interaction among polar molecules. The influence on the stopping cross section depends on the strength of these interactions; it varies from a few percent in the latter case up to 20% and more in a compound. These influences are the largest, if the velocity of the projectile is of the order of the average orbital velocity of the target atoms. (author)

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

    KAUST Repository

    Li, Wenjun

    2017-02-15

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

  6. Scanning probe and optical tweezer investigations of biomolecular interactions

    International Nuclear Information System (INIS)

    Rigby-Singleton, Shellie

    2002-01-01

    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located ∼0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin have

  7. Combinatorics of RNA-RNA interaction

    DEFF Research Database (Denmark)

    Li, Thomas J X; Reidys, Christian

    2012-01-01

    RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...

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

    Science.gov (United States)

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

    2015-01-01

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

  9. Molecular interactions in the betaine monohydrate-polyol deep eutectic solvents: Experimental and computational studies

    Science.gov (United States)

    Zahrina, Ida; Mulia, Kamarza; Yanuar, Arry; Nasikin, Mohammad

    2018-04-01

    DES (deep eutectic solvents) are a new class of ionic liquids that have excellent properties. The strength of interaction between molecules in the DES affects their properties and applications. In this work, the strength of molecular interactions between components in the betaine monohydrate salt and polyol (glycerol or/and propylene glycol) eutectic mixtures was studied by experimental and computational studies. The melting point and fusion enthalpy of the mixtures were measured using STA (Simultaneous Thermal Analyzer). The nature and strength of intermolecular interactions were observed by FT-IR and NMR spectroscopy. The molecular dynamics simulation was used to determine the number of H-bonds, percent occupancy, and radial distribution functions in the eutectic mixtures. The interaction between betaine monohydrate and polyol is following order: betaine monohydrate-glycerol-propylene glycol > betaine monohydrate-glycerol > betaine monohydrate-propylene glycol, where the latter is the eutectic mixture with the lowest stability, strength and extent of the hydrogen bonding interactions between component molecules. The presence of intra-molecular hydrogen bonding interactions, the inter-molecular hydrogen bonding interactions between betaine molecule and polyol, and also interactions between polyol and H2O of betaine monohydrate in the eutectic mixtures.

  10. An approach to the intermolecular energy in pure liquids

    Directory of Open Access Journals (Sweden)

    GAbriel Hernández de la Torre

    2010-07-01

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

  11. Competing intramolecular N-H⋯O=C hydrogen bonds and extended intermolecular network in 1-(4-chlorobenzoyl)-3-(2-methyl-4-oxopentan-2-yl) thiourea analyzed by experimental and theoretical methods

    Energy Technology Data Exchange (ETDEWEB)

    Saeed, Aamer, E-mail: aamersaeed@yahoo.com [Department of Chemistry, Quaid-I-Azam University, Islamabad 45320 (Pakistan); Khurshid, Asma [Department of Chemistry, Quaid-I-Azam University, Islamabad 45320 (Pakistan); Jasinski, Jerry P. [Department of Chemistry, Keene State College, 229 Main Street Keene, NH 03435-2001 (United States); Pozzi, C. Gustavo; Fantoni, Adolfo C. [Instituto de Física La Plata, Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 49 y 115, La Plata, Buenos Aires (Argentina); Erben, Mauricio F., E-mail: erben@quimica.unlp.edu.ar [CEQUINOR (UNLP, CONICET-CCT La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, C.C. 962, (1900) La Plata, Buenos Aires (Argentina)

    2014-03-18

    Highlights: • Two distinct N-H⋯O=C intramolecular competing hydrogen bonds are feasible in the title molecule. • Crystal structures and vibrational properties were determined. • The C=O and C=S double bonds of the acyl-thiourea group are mutually oriented in opposite directions. • A strong hyperconjugative lpO1 → σ{sup ∗}(N2-H) remote interaction was detected. • Topological analysis reveals a Cl⋯N interaction playing a relevant role in crystal packing. - Abstract: The synthesis of a novel 1-acyl-thiourea species (C{sub 14}H{sub 17}N{sub 2}O{sub 2}SCl), has been tailored in such a way that two distinct N-H⋯O=C intramolecular competing hydrogen bonds are feasible. The X-ray structure analysis as well as the vibrational (FT-IR and FT-Raman) data reveal that the S conformation is preferred, with the C=O and C=S bonds of the acyl-thiourea group pointing in opposite directions. The preference for the intramolecular N-H⋯O=C hydrogen bond within the -C(O)NHC(S)NH- core is confirmed. The Natural Bond Orbital and the Atom in Molecule approaches demonstrate that a strong hyperconjugative lpO → σ{sup ∗}(N-H) remote interaction between the acyl and the thioamide N-H groups is responsible for the stabilization of the S conformation. Intermolecular interactions have been characterized in the periodic system electron density and the topological analysis reveals the presence of an extended intermolecular network in the crystal, including a Cl⋯N interaction playing a relevant role in crystal packing.

  12. Equations of state of nonspherical fluids by spherical intermolecular potentials

    International Nuclear Information System (INIS)

    Bastea, S; Ree, F H

    1999-01-01

    The equilibrium properties of anisotropic molecular fluids can be in principle calculated in a statistical mechanics framework, but the theory is generally too cumbersome for many practical applications. Fortunately, at high densities and temperatures the anisotropy can be averaged-out by means of a density and temperature independent potential (the median) that produces reliable thermodynamics[1,2]. The proposal of Shaw and Johnson[1], which turns out to be the so-called median potential[2], is very successful in predicting the thermodynamics of simple fluids such as N(sub 2) and CO(sub 2) at reasonable high pressures and temperatures[3]. Lebowitz and Percus[2] pointed out some time ago that the success of this approximation could perhaps be understood in terms of a simple theory that treats the asphericity as a perturbation. The median appears to be the best choice for hard nonspherical potential[4], which may explain its success for fluids at high densities, where the hard core contribution is known to be dominant

  13. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    International Nuclear Information System (INIS)

    Alocci, Davide; Bernini, Andrea; Niccolai, Neri

    2013-01-01

    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

  14. Lattice and Molecular Vibrations in Single Crystal I2 at 77 K by Inelastic Neutron Scattering

    DEFF Research Database (Denmark)

    Smith, H. G.; Nielsen, Mourits; Clark, C. B.

    1975-01-01

    Phonon dispersion curves of single crystal iodine at 77 K have been measured by one-phonon coherent inelastic neutron scattering techniques. The data are analysed in terms of two Buckingham-six intermolecular potentials; one to represent the shortest intermolecular interaction (3.5 Å) and the other...

  15. An efficient method for the determination of fourth virial coefficient with Lennard-Jones (12-6) potential and its application

    Energy Technology Data Exchange (ETDEWEB)

    Mamedov, Bahtiyar A. [Department of Physics, Gaziosmanpaşa University, 60250, Tokat (Turkey); Somuncu, Elif; Askerov, Iskender M. [Department of Physics, Giresun University, Giresun (Turkey)

    2016-08-10

    In this work, a new theoretical approach is proposed for calculating fourth virial coefficient with Lennard-Jones potential. The established algorithm can be used to evaluate the thermodynamics properties and the intermolecular interaction potentials of liquids and gases with an improved accuracy. Note that the evaluation of the high-order virial coefficients is very valuable for accurate calculation of thermodynamic parameters. By using the suggested method, the fourth virial coefficient of CH{sub 4}, Ar, C{sub 2}H{sub 6} and SF{sub 6} molecules are evaluated. The calculation results are useful for accurate interpretation of the experimental data and of the determination of related physical properties.

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

    Directory of Open Access Journals (Sweden)

    Zheng-Yu Jiang

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-01

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

  18. The anisotropic potential of molecular hydrogen determined from the scattering of oriented H2 on inert gases

    International Nuclear Information System (INIS)

    Zandee, A.P.L.M.

    1977-01-01

    This thesis deals with an experiment aimed at determining the angle dependence of an intermolecular potential between H 2 molecule and a rare gas atom. The small relative difference in total collision cross section for beams of differently oriented H 2 molecules colliding with inert gas atoms in a scattering box is measured (anisotropy A). Through variation of the orientation and by studying its influence on the total collision cross sections, the angle dependence of the intermolecular potential can be arrived at

  19. Nucleus-nucleus potential with repulsive core and elastic scattering. Part 1. Nucleus-nucleus interaction potential

    International Nuclear Information System (INIS)

    Davidovs'ka, O.Yi.; Denisov, V.Yu.; Nesterov, V.O.

    2010-01-01

    Various approaches for nucleus-nucleus interaction potential evaluation are discussed in details. It is shown that the antisymmetrization of nucleons belonging to different nuclei and the Pauli principle give the essential contribution into the nucleus-nucleus potential at distances, when nuclei are strongly overlapping, and lead to appearance of the repulsive core of nucleus nucleus interaction at small distances between nuclei.

  20. Determination and Quantification of Molecular Interactions in Protein Films: A Review

    Directory of Open Access Journals (Sweden)

    Felicia Hammann

    2014-12-01

    Full Text Available Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography and analysis of solid films (spectroscopy techniques, X-ray scattering methods. To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

  1. Determination and Quantification of Molecular Interactions in Protein Films: A Review.

    Science.gov (United States)

    Hammann, Felicia; Schmid, Markus

    2014-12-10

    Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography) and analysis of solid films (spectroscopy techniques, X-ray scattering methods). To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

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

    Science.gov (United States)

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

    2014-10-01

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

  3. Nuclear electric quadrupole interactions in liquids entrapped in cavities

    Energy Technology Data Exchange (ETDEWEB)

    Furman, Gregory B., E-mail: gregoryf@bgu.ac.il; Meerovich, Victor M.; Sokolovsky, Vladimir L. [Ben Gurion University of the Negev, Physics Department (Israel)

    2016-12-15

    Liquids entrapped in cavities and containing quadrupole nuclei are considered. The interaction of the quadrupole moment of a nucleus with the electric field gradient is studied. In such a system, molecules are in both rotational and translational Brownian motions which are described by the diffusion equation. Solving this equation, we show that the intra- and intermolecular nuclear quadrupole interactions are averaged to zero in cavities with the size larger than several angstroms.

  4. Solitary wave exchange potential and nucleon-nucleon interaction

    International Nuclear Information System (INIS)

    Prema, K.; Raghavan, S.S.; Sekhar Raghavan

    1986-11-01

    Nucleon-nucleon interaction is studied using a phenomenological potential model called solitary wave exchange potential model. It is shown that this simple model reproduces the singlet and triplet scattering data and the deuteron parameters reasonably well. (author). 6 refs, 2 figs, 1 tab

  5. Synthesis and description of intermolecular interactions in new sulfonamide derivatives of tranexamic acid

    Science.gov (United States)

    Ashfaq, Muhammad; Arshad, Muhammad Nadeem; Danish, Muhammad; Asiri, Abdullah M.; Khatoon, Sadia; Mustafa, Ghulam; Zolotarev, Pavel N.; Butt, Rabia Ayub; Şahin, Onur

    2016-01-01

    Tranexamic acid (4-aminomethyl-cyclohexanecarboxylic acid) was reacted with sulfonyl chlorides to produce structurally related four sulfonamide derivatives using simple and environmental friendly method to check out their three-dimensional behavior and van der Walls interactions. The molecules were crystallized in different possibilities, as it is/after alkylation at its O and N atoms/along with a co-molecule. All molecules were crystallized in monoclinic crystal system with space group P21/n, P21/c and P21/a. X-ray studies reveal that the molecules stabilized themselves by different kinds of hydrogen bonding interactions. The molecules are getting connected through O-H⋯O hydrogen bonds to form inversion dimers which are further connected through N-H⋯O interactions. The molecules in which N and O atoms were alkylated showed non-classical interaction and generated centro-symmetric R22(24) ring motif. The co-crystallized host and guest molecules are connected to each other via O-H⋯O interactions to generate different ring motifs. By means of the ToposPro software an analysis of the topologies of underlying nets that correspond to molecular packings and hydrogen-bonded networks in structures under consideration was carried out.

  6. A 3D network of helicates fully assembled by pi-stacking interactions.

    Science.gov (United States)

    Vázquez, Miguel; Taglietti, Angelo; Gatteschi, Dante; Sorace, Lorenzo; Sangregorio, Claudio; González, Ana M; Maneiro, Marcelino; Pedrido, Rosa M; Bermejo, Manuel R

    2003-08-07

    The neutral dinuclear dihelicate [Cu2(L)2] x 2CH3CN (1) forms a unique 3D network in the solid state due to pi-stacking interactions, which are responsible for intermolecular antiferromagnetic coupling between Cu(II) ions.

  7. Potential disruption of protein-protein interactions by graphene oxide

    International Nuclear Information System (INIS)

    Feng, Mei; Kang, Hongsuk; Luan, Binquan; Yang, Zaixing; Zhou, Ruhong

    2016-01-01

    Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

  8. Potential disruption of protein-protein interactions by graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Mei [Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027 (China); Kang, Hongsuk; Luan, Binquan [Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Yang, Zaixing [Institute of Quantitative Biology and Medicine, SRMP and RAD-X, and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Zhou, Ruhong, E-mail: ruhong@us.ibm.com [Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027 (China); Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Department of Chemistry, Columbia University, New York, New York 10027 (United States)

    2016-06-14

    Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

  9. Diabatic interaction potential for nucleus-nucleus collisions

    International Nuclear Information System (INIS)

    Noerenberg, W.; Lukasiak, A.

    1984-01-01

    Within a refined method for the construction of diabatic states allowing for the treatment of the full spin-orbit coupling, characteristic features of the diabatic potential for nucleus-nucleus collisions are investigated. Approximately 90% of the strong repulsion results from diabatic particle-hole excitations, while only 10% is due to compression. The diabatic interaction potential describes a physical situation intermediate between adiabatic and sudden approximations. (orig.)

  10. Disorder and intermolecular interactions in a family of tetranuclear Ni(II) complexes probed by high-frequency electron paramagnetic resonance.

    Science.gov (United States)

    Lawrence, Jon; Yang, En-Che; Edwards, Rachel; Olmstead, Marilyn M; Ramsey, Chris; Dalal, Naresh S; Gantzel, Peter K; Hill, Stephen; Hendrickson, David N

    2008-03-17

    structure splittings for complex 3. This behavior is thought to be due to the onset of short-range magnetic correlations/coherences between molecules caused by weak intermolecular magnetic exchange interactions.

  11. Binaural interaction in auditory evoked potentials: Brainstem, middle- and long-latency components

    OpenAIRE

    McPherson, DL; Starr, A

    1993-01-01

    Binaural interaction occurs in the auditory evoked potentials when the sum of the monaural auditory evoked potentials are not equivalent to the binaural evoked auditory potentials. Binaural interaction of the early- (0-10 ms), middle- (10-50 ms) and long-latency (50-200 ms) auditory evoked potentials was studied in 17 normal young adults. For the early components, binaural interaction was maximal at 7.35 ms accounting for a reduction of 21% of the amplitude of the binaural evoked potentials. ...

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

    International Nuclear Information System (INIS)

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

    2003-01-01

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

  13. Computer Modeling of Halogen Bonds and Other sigma-Hole Interactions

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal H.; Hobza, Pavel

    2016-01-01

    Roč. 116, č. 9 (2016), s. 5155-5187 ISSN 0009-2665 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : density functional theory * adapted perturbation theory * intermolecular interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 47.928, year: 2016

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-12-31

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

  15. Stability of stationary states of non-local equations with singular interaction potentials

    KAUST Repository

    Fellner, Klemens

    2011-04-01

    We study the large-time behaviour of a non-local evolution equation for the density of particles or individuals subject to an external and an interaction potential. In particular, we consider interaction potentials which are singular in the sense that their first derivative is discontinuous at the origin.For locally attractive singular interaction potentials we prove under a linear stability condition local non-linear stability of stationary states consisting of a finite sum of Dirac masses. For singular repulsive interaction potentials we show the stability of stationary states of uniformly bounded solutions under a convexity condition.Finally, we present numerical simulations to illustrate our results. © 2010 Elsevier Ltd.

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

    International Nuclear Information System (INIS)

    Gerweck, V.

    1989-12-01

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

  17. Mixed micelles of 7,12-dioxolithocholic acid and selected hydrophobic bile acids: interaction parameter, partition coefficient of nitrazepam and mixed micelles haemolytic potential.

    Science.gov (United States)

    Poša, Mihalj; Tepavčević, Vesna

    2011-09-01

    The formation of mixed micelles built of 7,12-dioxolithocholic and the following hydrophobic bile acids was examined by conductometric method: cholic (C), deoxycholic (D), chenodeoxycholic (CD), 12-oxolithocholic (12-oxoL), 7-oxolithocholic (7-oxoL), ursodeoxycholic (UD) and hiodeoxycholic (HD). Interaction parameter (β) in the studied binary mixed micelles had negative value, suggesting synergism between micelle building units. Based on β value, the hydrophobic bile acids formed two groups: group I (C, D and CD) and group II (12-oxoL, 7-oxoL, UD and HD). Bile acids from group II had more negative β values than bile acids from group I. Also, bile acids from group II formed intermolecular hydrogen bonds in aggregates with both smaller (2) and higher (4) aggregation numbers, according to the analysis of their stereochemical (conformational) structures and possible structures of mixed micelles built of these bile acids and 7,12-dioxolithocholic acid. Haemolytic potential and partition coefficient of nitrazepam were higher in mixed micelles built of the more hydrophobic bile acids (C, D, CD) and 7,12-dioxolithocholic acid than in micelles built only of 7,12-dioxolithocholic acid. On the other hand, these mixed micelles still had lower values of haemolytic potential than micelles built of C, D or CD. The mixed micelles that included bile acids: 12-oxoL, 7-oxoL, UD or HD did not significantly differ from the micelles of 7,12-dioxolithocholic acid, observing the values of their haemolytic potential. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH32BH3 and KN(CH32BH3

    Directory of Open Access Journals (Sweden)

    Filip Sagan

    2016-03-01

    Full Text Available In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH32BH3 and KN(CH32BH3 was performed by means of the charge and energy decomposition method (ETS-NOCV as well as the Interacting Quantum Atoms (IQA approach. It was determined that both crystals are stabilized by electrostatically dominated intra- and intermolecular M∙∙∙H–B interactions (M = Li, K. For LiN(CH32BH3 the intramolecular charge transfer appeared (B–H→Li to be more pronounced compared with the corresponding intermolecular contribution. We clarified for the first time, based on the ETS-NOCV and IQA methods, that homopolar BH∙∙∙HB interactions in LiN(CH32BH3 can be considered as destabilizing (due to the dominance of repulsion caused by negatively charged borane units, despite the fact that some charge delocalization within BH∙∙∙HB contacts is enforced (which explains H∙∙∙H bond critical points found from the QTAIM method. Interestingly, quite similar (to BH∙∙∙HB intermolecular homopolar dihydrogen bonds CH∙∙∙HC appared to significantly stabilize both crystals—the ETS-NOCV scheme allowed us to conclude that CH∙∙∙HC interactions are dispersion dominated, however, the electrostatic and σ/σ*(C–H charge transfer contributions are also important. These interactions appeared to be more pronounced in KN(CH32BH3 compared with LiN(CH32BH3.

  19. Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic.

    Science.gov (United States)

    Chaudhari, Mangesh I; Holleran, Sinead A; Ashbaugh, Henry S; Pratt, Lawrence R

    2013-12-17

    The osmotic second virial coefficients, B2, for atomic-sized hard spheres in water are attractive (B2 attractive with increasing temperature (ΔB2/ΔT attractive and endothermic at moderate temperatures. Hydrophobic interactions between atomic-sized hard spheres in water are more attractive than predicted by the available statistical mechanical theory. These results constitute an initial step toward detailed molecular theory of additional intermolecular interaction features, specifically, attractive interactions associated with hydrophobic solutes.

  20. Calculation of Rydberg interaction potentials

    DEFF Research Database (Denmark)

    Weber, Sebastian; Tresp, Christoph; Menke, Henri

    2017-01-01

    for calculating the required electric multipole moments and the inclusion of electromagnetic fields with arbitrary direction. We focus specifically on symmetry arguments and selection rules, which greatly reduce the size of the Hamiltonian matrix, enabling the direct diagonalization of the Hamiltonian up...... to higher multipole orders on a desktop computer. Finally, we present example calculations showing the relevance of the full interaction calculation to current experiments. Our software for calculating Rydberg potentials including all features discussed in this tutorial is available as open source....

  1. Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Hobza, Pavel

    2016-01-01

    Roč. 116, č. 9 (2016), s. 5038-5071 ISSN 0009-2665 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : density functional theory * coupled cluster theory * intermolecular interaction energies Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 47.928, year: 2016

  2. Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

    Science.gov (United States)

    Crawford, Lisa; Karr, Laurel J.; Nadarajah, Arunan; Pusey, Marc

    1999-01-01

    A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

  3. Potential drug-drug interactions on in-patient medication ...

    African Journals Online (AJOL)

    Potential drug-drug interactions on in-patient medication prescriptions at Mbarara Regional Referral Hospital (MRRH) in western Uganda: prevalence, clinical importance and associated factors. SJ Lubinga, E Uwiduhaye ...

  4. Coiodação de alquenos com nucleófilos oxigenados: reações intermoleculares

    Directory of Open Access Journals (Sweden)

    Sanseverino Antonio Manzolillo

    2001-01-01

    Full Text Available A review on the electrophilic addition of iodine to alkenes in the presence of oxygen containing nucleophiles (cohalogenation reaction is presented. The intermolecular reactions are discussed with emphasis in methods of reaction and synthetic applications of the resulting vicinal iodo-functionalized products (iodohydrins, beta-iodoethers and beta-iodocarboxylates.

  5. Analytical local electron-electron interaction model potentials for atoms

    International Nuclear Information System (INIS)

    Neugebauer, Johannes; Reiher, Markus; Hinze, Juergen

    2002-01-01

    Analytical local potentials for modeling the electron-electron interaction in an atom reduce significantly the computational effort in electronic structure calculations. The development of such potentials has a long history, but some promising ideas have not yet been taken into account for further improvements. We determine a local electron-electron interaction potential akin to those suggested by Green et al. [Phys. Rev. 184, 1 (1969)], which are widely used in atom-ion scattering calculations, electron-capture processes, and electronic structure calculations. Generalized Yukawa-type model potentials are introduced. This leads, however, to shell-dependent local potentials, because the origin behavior of such potentials is different for different shells as has been explicated analytically [J. Neugebauer, M. Reiher, and J. Hinze, Phys. Rev. A 65, 032518 (2002)]. It is found that the parameters that characterize these local potentials can be interpolated and extrapolated reliably for different nuclear charges and different numbers of electrons. The analytical behavior of the corresponding localized Hartree-Fock potentials at the origin and at long distances is utilized in order to reduce the number of fit parameters. It turns out that the shell-dependent form of Green's potential, which we also derive, yields results of comparable accuracy using only one shell-dependent parameter

  6. Anandamide-ceramide interactions in a membrane environment: Molecular dynamic simulations data.

    Science.gov (United States)

    Di Scala, Coralie; Mazzarino, Morgane; Yahi, Nouara; Varini, Karine; Garmy, Nicolas; Fantini, Jacques; Chahinian, Henri

    2017-10-01

    Anandamide is a lipid neurotransmitter that interacts with various plasma membrane lipids. The data here consists of molecular dynamics simulations of anandamide, C18-ceramide and cholesterol performed in vacuo and within a hydrated palmitoyl-oleoyl-phosphatidylcholine (POPC)/cholesterol membrane. Several models of anandamide/cholesterol and anandamide/ceramide complexes are presented. The energy of interaction and the nature of the intermolecular forces involved in each of these complexes are detailed. The impact of water molecules hydrating the POPC/cholesterol membrane for the stability of the anandamide/cholesterol and anandamide/ceramide complexes is also analyzed. From a total number of 1920 water molecules stochatiscally merged with the lipid matrix, 48 were eventually redistributed around the polar head groups of the anandamide/ceramide complex, whereas only 15 reached with the anandamide/cholesterol complex. The interpretation of this dataset is presented in the accompanying article "Ceramide binding to anandamide increases its half-life and potentiates its cytotoxicity in human neuroblastoma cells" [1].

  7. Interactions of molecules and the properties of crystals

    Science.gov (United States)

    McConnell, Thomas Daniel Leigh

    In this thesis the basic theory of the lattice dynamics of molecular crystals is considered, with particular reference to the specific case of linear molecules. The objective is to carry out a critical investigation of a number of empirical potentials as models for real systems. Suitable coordinates are introduced, in particular vibrational coordinates which are used to describe the translational and rotational modes of the free molecule. The Taylor expansion of the intermolecular potential is introduced and its terms considered, in particular the (first-order) equilibrium conditions for such a system and the (second-order) lattice vibrations. The elastic properties are also considered, in particular with reference to the specific case of rhombohedral crystals. The compressibility and a number of conditions for elastic stability are introduced. The total intermolecular interaction potential is divided into three components using perturbation methods, the electrostatic energy, the repulsion energy and the dispersion energy. A number of models are introduced for these various components. The induction energy is neglected. The electrostatic interaction is represented by atomic multipole and molecular multipole models. The repulsion and dispersion energies are modelled together in a central interaction potential, either the Lennard-Jones atom-atom potential or the anisotropic Berne-Pechukas molecule-molecule potential. In each case, the Taylor expansion coefficients, used to calculate the various molecular properties, are determined. An algorithm is described which provides a relatively simple method for calculating cartesian tensors, which are found in the Taylor expansion coefficients of the multipolar potentials. This proves to be particularly useful from a computational viewpoint, both in terms of programming and calculating efficiency. The model system carbonyl sulphide is introduced and its lattice properties are described. Suitable parameters for potentials used

  8. Comparison of biomolecules on the basis of Molecular Interaction Potentials

    Directory of Open Access Journals (Sweden)

    Rodrigo Jordi

    2002-01-01

    Full Text Available Molecular Interaction Potentials (MIP are frequently used for the comparison of series of compounds displaying related biological behaviors. These potentials are interaction energies between the considered compounds and relevant probes. The interaction energies are computed in the nodes of grids defined around the compounds. There is a need of detailed and objective comparative analyses of MIP distributions in the framework of structure-activity studies. On the other hand, MIP-based studies do not have to be restricted to series of small ligands, since such studies present also interesting possibilities for the analysis and comparison of biological macromolecules. Such analyses can benefit from the application of new methods and computational approaches. The new software MIPSim (Molecular Interaction Potentials Similarity analysis has recently been introduced with the purpose of analyzing and comparing MIP distributions of series of biomolecules. This program is transparently integrated with other programs, like GAMESS or GRID, which can be used for the computation of the potentials to be analyzed or compared. MIPSim incorporates several definitions of similarity coefficients, and is capable of combining several similarity measures into a single one. On the other hand, MIPSim can perform automatic explorations of the maximum similarity alignments between pairs of molecules.

  9. Market potential for interactive audio-visual media

    NARCIS (Netherlands)

    Leurdijk, A.; Limonard, S.

    2005-01-01

    NM2 (New Media for a New Millennium) develops tools for interactive, personalised and non-linear audio-visual content that will be tested in seven pilot productions. This paper looks at the market potential for these productions from a technological, a business and a users' perspective. It shows

  10. The potential of protein-nanomaterial interaction for advanced drug delivery.

    Science.gov (United States)

    Peng, Qiang; Mu, Huiling

    2016-03-10

    Nanomaterials, like nanoparticles, micelles, nano-sheets, nanotubes and quantum dots, have great potentials in biomedical fields. However, their delivery is highly limited by the formation of protein corona upon interaction with endogenous proteins. This new identity, instead of nanomaterial itself, would be the real substance the organs and cells firstly encounter. Consequently, the behavior of nanomaterials in vivo is uncontrollable and some undesired effects may occur, like rapid clearance from blood stream; risk of capillary blockage; loss of targeting capacity; and potential toxicity. Therefore, protein-nanomaterial interaction is a great challenge for nanomaterial systems and should be inhibited. However, this interaction can also be used to functionalize nanomaterials by forming a selected protein corona. Unlike other decoration using exogenous molecules, nanomaterials functionalized by selected protein corona using endogenous proteins would have greater promise for clinical use. In this review, we aim to provide a comprehensive understanding of protein-nanomaterial interaction. Importantly, a discussion about how to use such interaction is launched and some possible applications of such interaction for advanced drug delivery are presented. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

    Science.gov (United States)

    Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

    2018-04-01

    The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

  12. Intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization reactions of 1,6-enynes with symmetrical and unsymmetrical alkynes†

    Science.gov (United States)

    Andrew Evans, P.; Sawyer, James R.; Lai, Kwong Wah; Huffman, John C.

    2006-01-01

    The crossed intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization of carbon and heteroatom tethered 1,6-enynes can be accomplished with symmetrical and unsymmetrical alkynes, to afford the corresponding bicyclohexadienes in an efficient and highly selective manner. PMID:16075089

  13. N-Oxide-N-oxide interactions and Cl...Cl halogen bonds in pentachloropyridine N-oxide: the many-body approach to interactions in the crystal state.

    Science.gov (United States)

    Wzgarda-Raj, Kinga; Rybarczyk-Pirek, Agnieszka J; Wojtulewski, Sławomir; Palusiak, Marcin

    2018-02-01

    Pentachloropyridine N-oxide, C 5 Cl 5 NO, crystallizes in the monoclinic space group P2 1 /c. In the crystal structure, molecules are linked by C-Cl...Cl halogen bonds into infinite ribbons extending along the crystallographic [100] direction. These molecular aggregates are further stabilized by very short intermolecular N-oxide-N-oxide interactions into herringbone motifs. Computations based on quantum chemistry methods allowed for a more detailed description of the N-oxide-N-oxide interactions and Cl...Cl halogen bonds. For this purpose, Hirshfeld surface analysis and the many-body approach to interaction energy were applied.

  14. CP/MAS 13C NMR characterization of the isomeric states and intermolecular packing in tris(8-hydroxyquinoline) aluminum(III) (Alq3).

    Science.gov (United States)

    Kaji, Hironori; Kusaka, Yasunari; Onoyama, Goro; Horii, Fumitaka

    2006-04-05

    The isomeric states and intermolecular packing of tris(8-hydroxyquinoline) aluminum(III) (Alq(3)) in the alpha-, gamma-, and delta-crystalline forms and in the amorphous state, which are important for understanding the light-emitting and electron-transport properties, have been analyzed by CP/MAS (13)C NMR. This simple NMR experiment shows that the isomeric state of alpha- and amorphous Alq(3) is meridional, whereas that of gamma- and delta-Alq(3) is facial. In the amorphous Alq(3), the inclusion of facial isomers has been under debate. Our experiments show that meridional isomers are dominant in the amorphous Alq(3), although the existence of facial isomers cannot be completely denied. The local structure of amorphous Alq(3) is similar to that of alpha-Alq(3) and is significantly different from those of gamma- and delta-Alq(3). Among these Alq(3) samples, the effect of intermolecular interaction is not found only for gamma-Alq(3). This finding can explain the good solvent solubility of gamma-Alq(3), compared with the other crystalline forms. It is also shown that the structures are locally disordered not only for amorphous Alq(3) but also for alpha-Alq(3), although clear X-ray diffraction peaks are observed for alpha-Alq(3). In contrast, the local structures of gamma- and delta-Alq(3) are well defined. A clear relation is found between the spectral patterns of CP/MAS (13)C NMR and the fluorescence wavelengths; the samples, which consist of facial isomers, show blue-shifted fluorescence compared with those of meridionals.

  15. Intermolecular Interactions at high pressure

    DEFF Research Database (Denmark)

    Eikeland, Espen Zink

    2016-01-01

    In this project high-pressure single crystal X-ray diffraction has been combined with quantitative energy calculations to probe the energy landscape of three hydroquinone clathrates enclosing different guest molecules. The simplicity of the hydroquinone clathrate structures together with their st...

  16. Magnetic interactions in iron (III) porphyrin chlorides

    International Nuclear Information System (INIS)

    Ernst, J.; Subramanian, Japyesan; Fuhrhop, J.H.

    1977-01-01

    Intermolecular exchange interactions in iron(III) porphyrin chlorides (porphyrin = OEP, proto, TPP) have been studied by X-ray structure, EPR and magnetic susceptibility studies. The crystal structure of Fe(III)OEP-Cl was found to be different from that of the other two. Different types of exchange broadened EPR-spectra are obtained which are attributable to the arrangement in the crystals. The EPR results correlate well with magnetic susceptibility data. (orig.) [de

  17. Synthesis of benzimidazoles by potassium tert-butoxide-promoted intermolecular cyclization reaction of 2-iodoanilines with nitriles.

    Science.gov (United States)

    Xiang, Shi-Kai; Tan, Wen; Zhang, Dong-Xue; Tian, Xian-Li; Feng, Chun; Wang, Bi-Qin; Zhao, Ke-Qing; Hu, Ping; Yang, Hua

    2013-11-14

    The synthesis of benzimidazoles by intermolecular cyclization reaction of 2-iodoanilines with nitriles has been developed. These reactions proceeded without the aid of any transition metals or ligands and just using KOBu(t) as the base. A variety of substituted benzimidazole derivatives can be synthesized by the approach.

  18. Basis Set Dependence of Interaction Energies Computed Using Composite Post-MP2 Methods

    Czech Academy of Sciences Publication Activity Database

    Platts, J. A.; Hill, J. G.; Riley, K. E.; Řezáč, Jan; Hobza, Pavel

    2013-01-01

    Roč. 9, č. 1 (2013), s. 330-337 ISSN 1549-9618 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : plesset perturbation-theory * intermolecular interaction energies * density fitting approximations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013

  19. Scattering of neutral metal clusters: Long-range interactions and response properties

    International Nuclear Information System (INIS)

    Kresin, V.V.; Scheidemann, A.

    1993-01-01

    The absolute integral cross sections for low-energy collisions of neutral sodium clusters Na n (n=2--40) with atoms and molecules (Ar, N 2 , O 2 , and halogens) have been measured. The cross sections are found to be exceptionally large (up to thousands of square angstroms), showing the dominant role of long-range intermolecular interactions. Elastic scattering proceeding under the influence of the van der Waals force, and a reaction channel involving electron transfer can successfully describe the measurements. The strength of the van der Waals potential is defined by such cluster response properties as the electric polarizability and the frequency of the giant dipole resonance. The reactive electron-jump channel, in turn, is described by the ''harpooning'' mechanism which is sensitive to the cluster ionization potential. Employing parameters taken from spectroscopic studies of alkali clusters, we obtain good agreement with the observed cross sections. This provides a direct connection between beam scattering experiments and studies of cluster electromagnetic response properties

  20. Intermolecular Interactions in Binary Liquid Mixtures of Styrene with m-, o-, or p-xylene%苯乙烯与邻、间、对-二甲苯二元混合液的分子间相互作用

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The densities (ρ), ultrasonic speeds (v), and refractive indices (n) of binary mixtures of styrene (STY)with m-, o-, or p-xylene, including those of their pure liquids, were measured over the entire composition range at the temperatures 298.15, 303.15, 308.15, and 313.15 K. The excess volumes (VE), deviations in isentropic compressibilities(△ks), acoustic impedances (△Z), and refractive indices (△n) were calculated from the experimental data. Partial molar volumes (V0φ,2) and partial molar isentropic compressibilities (K0φ,2) of xylenes in styrene have also been calculated. The derived functions, namely, VE, △ks, △Z, △n, V0φ,2, and K0φ,2 were used to have a better understanding of the intermolecular interactions occurring between the component molecules of the present liquid mixtures. The variations of these parameters suggest that the interactions between styrene and o-, m-, or p-xylene molecules follow the sequences: p-xylene>o-xylene>m-xylene. Apart from using density data for the calculation of VE, excess molar volumes were also estimated using refractive index data. Furthermore, several refractive index mixing rules have been used to estimate the refractive indices of the studied liquid mixtures theoretically. Overall, the computed and measured data were interpreted in terms of interactions between the mixing components.

  1. Potential drug interactions in patients given antiretroviral therapy.

    Science.gov (United States)

    Santos, Wendel Mombaque Dos; Secoli, Silvia Regina; Padoin, Stela Maris de Mello

    2016-11-21

    to investigate potential drug-drug interactions (PDDI) in patients with HIV infection on antiretroviral therapy. a cross-sectional study was conducted on 161 adults with HIV infection. Clinical, socio demographic, and antiretroviral treatment data were collected. To analyze the potential drug interactions, we used the software Micromedex(r). Statistical analysis was performed by binary logistic regression, with a p-value of ≤0.05 considered statistically significant. of the participants, 52.2% were exposed to potential drug-drug interactions. In total, there were 218 potential drug-drug interactions, of which 79.8% occurred between drugs used for antiretroviral therapy. There was an association between the use of five or more medications and potential drug-drug interactions (p = 0.000) and between the time period of antiretroviral therapy being over six years and potential drug-drug interactions (p central nervous and cardiovascular systems, but also can interfere in tests used for detection of HIV resistance to antiretroviral drugs. investigar potenciais interações droga-droga (PDDI) em pacientes infectados com HIV em terapia de antirretroviral. um estudo de corte transversal foi conduzido em 161 pessoas infectadas com o HIV. Dados de tratamentos clínicos, sociodemográficos e antirretrovirais foram coletados. Para analisar a possível interação medicamentosa, nós usamos o software Micromedex(r). A análise estatística foi feita por regressão logística binária, com um valor P de ≤0.05, considerado estatisticamente significativo. dos participantes, 52.2% foram expostos a potenciais interações droga-droga. No total, houve 218 interações droga-droga, das quais 79.8% ocorreram entre drogas usadas para a terapia antirretroviral. Houve uma associação entre o uso de cinco ou mais medicamentos e possíveis interações droga-droga (p = 0.000), e entre o período de tempo de terapia antirretroviral acima de seis anos e possíveis interações droga

  2. Repulsive baryonic interactions and lattice QCD observables at imaginary chemical potential

    Directory of Open Access Journals (Sweden)

    Volodymyr Vovchenko

    2017-12-01

    Full Text Available The first principle lattice QCD methods allow to calculate the thermodynamic observables at finite temperature and imaginary chemical potential. These can be compared to the predictions of various phenomenological models. We argue that Fourier coefficients with respect to imaginary baryochemical potential are sensitive to modeling of baryonic interactions. As a first application of this sensitivity, we consider the hadron resonance gas (HRG model with repulsive baryonic interactions, which are modeled by means of the excluded volume correction. The Fourier coefficients of the imaginary part of the net-baryon density at imaginary baryochemical potential – corresponding to the fugacity or virial expansion at real chemical potential – are calculated within this model, and compared with the Nt=12 lattice data. The lattice QCD behavior of the first four Fourier coefficients up to T≃185 MeV is described fairly well by an interacting HRG with a single baryon–baryon eigenvolume interaction parameter b≃1 fm3, while the available lattice data on the difference χ2B−χ4B of baryon number susceptibilities is reproduced up to T≃175 MeV. Keywords: Hadron resonance gas, Excluded volume, Imaginary chemical potential

  3. Interaction potentials and their effect on crystal nucleation and symmetry

    International Nuclear Information System (INIS)

    Hsu, C.S.; Rahman, A.

    1979-01-01

    Molecular dynamics technique has been used to study the effect of the interaction potential on crystal nucleation and the symmetry of the nucleated phase. Four systems, namely rubidium, Lennard-Jones, rubidium-truncated, and Lennard-Jones-truncated, have been studied each at reduced density 0.95. Two types of calculations were performed. Firstly, starting from a liquid state, each system was quenched rapidly to a reduced temperature of approx.0.1. The nucleation process for these systems was monitored by studying the time dependence of temperature and the pair correlation function, and the resulting crystalline structure analyzed using among other properties the Voronoi polyhedra. Only in the case of rubidium was a b.c.c. structure nucleated. In the other three cases we obtained a f.c.c. ordering. Secondly, we have studied the effect of changing the interaction potential in a system which has already achieved an ordered state under the action of some other potential. After establishing a b.c.c. structure in a rubidium system, the change in the symmetry of the system was studied when the pair potential was modified to one of the other three forms. The results from both types of calculations are consistent: the rubidium potential leads to a b.c.c. structure while the other three potentials give an f.c.c. structure. Metastable disordered structures were not obtained in any of the calculations. However, the time elapse between the moment when the system is quick-quenched and the moment when nucleation occurs appears to depend upon the potential of interaction

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1990-01-31

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

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

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  6. Highly Convergent Total Synthesis of (+)-Lithospermic Acid via a Late-Stage Intermolecular C–H Olefination

    Science.gov (United States)

    Wang, Dong-Hui; Yu, Jin-Quan

    2011-01-01

    The total synthesis of (+)-lithospermic acid is reported, which exploits two successive C–H activation reactions as the key steps. Rh-catalyzed carbene C–H insertion reaction using Davies’ catalyst built the dihydrobenzofuran core, and a late-stage intermolecular C–H olefination coupled the olefin unit with the dihydrobenzofuran core to construct the molecule in a highly convergent manner. PMID:21443224

  7. Are Noncovalent Interactions an Achilles Heel in Chemistry Education? A Comparison of Instructional Approaches

    Science.gov (United States)

    Williams, Leah C.; Underwood, Sonia M.; Klymkowsky, Michael W.; Cooper, Melanie M.

    2015-01-01

    Intermolecular forces (IMFs), or more broadly, noncovalent interactions either within or between molecules, are central to an understanding of a wide range of chemical and biological phenomena. In this study, we present a multiyear, multi-institutional, longitudinal comparison of how students enrolled in traditional general chemistry courses and…

  8. Performance of Several Density Functional Theory Methods on Describing Hydrogen-Bond Interactions.

    Science.gov (United States)

    Rao, Li; Ke, Hongwei; Fu, Gang; Xu, Xin; Yan, Yijing

    2009-01-13

    We have investigated eleven density functionals, including LDA, PBE, mPWPW91, TPSS, B3LYP, X3LYP, PBE0, O3LYP, B97-1, MPW1K, and TPSSh, for their performances on describing hydrogen bond (HB) interactions. The emphasis has been laid not only on their abilities to calculate the intermolecular hydrogen bonding energies but also on their performances in predicting the relative energies of intermolecular H-bonded complexes and the conformer stabilities due to intramolecular hydrogen bondings. As compared to the best theoretical values, we found that although PBE and PBE0 gave the best estimation of HB strengths, they might fail to predict the correct order of relative HB energies, which might lead to a wrong prediction of the global minimum for different conformers. TPSS and TPSSh did not always improve over PBE and PBE0. B3LYP was found to underestimate the intermolecular HB strengths but was among the best performers in calculating the relative HB energies. We showed here that X3LYP and B97-1 were able to give good values for both absolute HB strengths and relative HB energies, making these functionals good candidates for HB description.

  9. [Potential antimicrobial drug interactions in clinical practice: consequences of polypharmacy and multidrug resistance].

    Science.gov (United States)

    Martínez-Múgica, Cristina

    2015-12-01

    Polypharmacy is a growing problem nowadays, which can increase the risk of potential drug interactions, and result in a loss of effectiveness. This is particularly relevant to the anti-infective therapy, especially when infection is produced by resistant bacteria, because therapeutic options are limited and interactions can cause treatment failure. All antimicrobial prescriptions were retrospectively reviewed during a week in the Pharmacy Department, in order to detect potential drug-interactions and analysing their clinical significance. A total of 314 antimicrobial prescriptions from 151 patients were checked. There was at least one potential interaction detected in 40% of patients, being more frequent and severe in those infected with multidrug-resistant microorganisms. Drugs most commonly involved were quinolones, azoles, linezolid and vancomycin. Potential drug interactions with antimicrobial agents are a frequent problem that can result in a loss of effectiveness. This is why they should be detected and avoided when possible, in order to optimize antimicrobial therapy, especially in case of multidrug resistant infections.

  10. TOWARDS PHASE TRANSFERABLE POTENTIAL FUNCTIONS - METHODOLOGY AND APPLICATION TO NITROGEN

    NARCIS (Netherlands)

    JORDAN, PC; VAN MAAREN, PJ; MAVRI, J; VAN DER SPOEL, D; BERENDSEN, HJC

    1995-01-01

    We describe a generalizable approach to the development of phase transferable effective intermolecular potentials and apply the method to the study of N-2 The method is based on a polarizable shell model description of the isolated molecule and uses experimental data to establish the parameters.

  11. Potential games and interactive decisions with multiple criteria

    NARCIS (Netherlands)

    Voorneveld, M.

    1999-01-01

    Game theory is a mathematical theory for analyzing strategic interaction between decision makers. This thesis covers two game-theoretic topics. The first part of this thesis deals with potential games: noncooperative games in which the information about the goals of the separate players that is

  12. The potential of protein-nanomaterial interaction for advanced drug delivery

    DEFF Research Database (Denmark)

    Peng, Qiang; Mu, Huiling

    2016-01-01

    Nanomaterials, like nanoparticles, micelles, nano-sheets, nanotubes and quantum dots, have great potentials in biomedical fields. However, their delivery is highly limited by the formation of protein corona upon interaction with endogenous proteins. This new identity, instead of nanomaterial itself...... of such interaction for advanced drug delivery are presented........ Therefore, protein-nanomaterial interaction is a great challenge for nanomaterial systems and should be inhibited. However, this interaction can also be used to functionalize nanomaterials by forming a selected protein corona. Unlike other decoration using exogenous molecules, nanomaterials functionalized...

  13. Hybrid approaches to nanometer-scale patterning: Exploiting tailored intermolecular interactions

    International Nuclear Information System (INIS)

    Mullen, Thomas J.; Srinivasan, Charan; Shuster, Mitchell J.; Horn, Mark W.; Andrews, Anne M.; Weiss, Paul S.

    2008-01-01

    In this perspective, we explore hybrid approaches to nanometer-scale patterning, where the precision of molecular self-assembly is combined with the sophistication and fidelity of lithography. Two areas - improving existing lithographic techniques through self-assembly and fabricating chemically patterned surfaces - will be discussed in terms of their advantages, limitations, applications, and future outlook. The creation of such chemical patterns enables new capabilities, including the assembly of biospecific surfaces to be recognized by, and to capture analytes from, complex mixtures. Finally, we speculate on the potential impact and upcoming challenges of these hybrid strategies.

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

    International Nuclear Information System (INIS)

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

    2012-01-01

    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 (CH 3 COCH 3 ) 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.

  15. A reactive empirical bond order (REBO) potential for hydrocarbon-oxygen interactions

    International Nuclear Information System (INIS)

    Ni, Boris; Lee, Ki-Ho; Sinnott, Susan B

    2004-01-01

    The expansion of the second-generation reactive empirical bond order (REBO) potential for hydrocarbons, as parametrized by Brenner and co-workers, to include oxygen is presented. This involves the explicit inclusion of C-O, H-O, and O-O interactions to the existing C-C, C-H, and H-H interactions in the REBO potential. The details of the expansion, including all parameters, are given. The new, expanded potential is then applied to the study of the structure and chemical stability of several molecules and polymer chains, and to modelling chemical reactions among a series of molecules, within classical molecular dynamics simulations

  16. Metal-Catalyzed Intra- and Intermolecular Addition of Carboxylic Acids to Alkynes in Aqueous Media: A Review

    Directory of Open Access Journals (Sweden)

    Javier Francos

    2017-11-01

    Full Text Available The metal-catalyzed addition of carboxylic acids to alkynes is a very effective tool for the synthesis of carboxylate-functionalized olefinic compounds in an atom-economical manner. Thus, a large variety of synthetically useful lactones and enol-esters can be accessed through the intra- or intermolecular versions of this process. In order to reduce the environmental impact of these reactions, considerable efforts have been devoted in recent years to the development of catalytic systems able to operate in aqueous media, which represent a real challenge taking into account the tendency of alkynes to undergo hydration in the presence of transition metals. Despite this, different Pd, Pt, Au, Cu and Ru catalysts capable of promoting the intra- and intermolecular addition of carboxylic acids to alkynes in a selective manner in aqueous environments have appeared in the literature. In this review article, an overview of this chemistry is provided. The synthesis of β-oxo esters by catalytic addition of carboxylic acids to terminal propargylic alcohols in water is also discussed.

  17. Interactions of C+(2PJ) with rare gas atoms: incipient chemical interactions, potentials and transport coefficients

    Science.gov (United States)

    Tuttle, William D.; Thorington, Rebecca L.; Viehland, Larry A.; Breckenridge, W. H.; Wright, Timothy G.

    2018-03-01

    Accurate interatomic potentials were calculated for the interaction of a singly charged carbon cation, C+, with a single rare gas atom, RG (RG = Ne-Xe). The RCCSD(T) method and basis sets of quadruple-ζ and quintuple-ζ quality were employed; each interaction energy was counterpoise corrected and extrapolated to the basis set limit. The lowest C+(2P) electronic term of the carbon cation was considered, and the interatomic potentials calculated for the diatomic terms that arise from these: 2Π and 2Σ+. Additionally, the interatomic potentials for the respective spin-orbit levels were calculated, and the effect on the spectroscopic parameters was examined. In doing this, anomalously large spin-orbit splittings for RG = Ar-Xe were found, and this was investigated using multi-reference configuration interaction calculations. The latter indicated a small amount of RG → C+ electron transfer and this was used to rationalize the observations. This is taken as evidence of an incipient chemical interaction, which was also examined via contour plots, Birge-Sponer plots and various population analyses across the C+-RG series (RG = He-Xe), with the latter showing unexpected results. Trends in several spectroscopic parameters were examined as a function of the increasing atomic number of the RG atom. Finally, each set of RCCSD(T) potentials was employed, including spin-orbit coupling to calculate the transport coefficients for C+ in RG, and the results were compared with the limited available data. This article is part of the theme issue `Modern theoretical chemistry'.

  18. Structural and interactional behaviour of aqueous mixture of room temperature ionic liquid; 2-hydroxyethyl-trimethylammonium L-lactate

    International Nuclear Information System (INIS)

    Chaudhary, Ganga Ram; Bansal, Shafila; Mehta, S.K.; Ahluwalia, A.S.

    2014-01-01

    Highlights: • Thermophysical and spectroscopic properties of aqueous mixtures 2-[HE3MA]LAC have been measured. • Effect of temperature on thermophysical properties has also been studied. • Stronger intermolecular have been observed between [HE3MA]LAC and H 2 O. • Magnitude of interactions decreases with the rise in temperature. • Spectroscopic studies shows interactions between -N + -(CH 3 ) 3 with -OH - group and COO − with -H + of IL and H 2 O. - Abstract: In order to understand the molecular interactions between the green solvent system, (water + lactate based ionic liquid); 2-hydroxyethyl-trimethylammonium L-lactate ([(C 2 H 4 OH)(CH 3 ) 3 N][Lactate]), the thermophysical properties viz. density ρ, speed of sound u, specific conductivity κ, refractive index n D and spectroscopic properties viz. IR, 1 H and 13 C NMR have been investigated over the whole composition range at atmospheric pressure with temperature varied from (293.15 to 323.15) K. To gain more insight of intermolecular interactions occurring in the aqueous mixture of [(C 2 H 4 OH)(CH 3 ) 3 N][Lactate], intermolecular free length L f , acoustic impedance Z, relative association R A , excess molar volume V E , deviations in isentropic compressibility ΔK S , partial molar excess volume V i E , partial molar deviations in isentropic compressibility ΔK S,i , deviation in specific conductivity Δκ and deviation in refractive index Δn D have been predicted as a function of IL concentration over the whole composition range. These results have been fitted to the Redlich–Kister polynomial. A large deviation from ideality has been observed on mixing water and [(C 2 H 4 OH)(CH 3 ) 3 N][Lactate] which are due to the formation of strong intermolecular hydrogen bonding between the two molecules. Also, it has been noticed that the mixture of water and [(C 2 H 4 OH)(CH 3 ) 3 N][Lactate] became warm that indicates mixing of these two components is exothermic. Thermodynamic and spectroscopic data

  19. DFT study of the interaction between 3-nitro-1,2,4-triazole-5-one and hydrogen fluoride

    International Nuclear Information System (INIS)

    Fang Guoyong; Xu Lina; Hu Xingen; Li Xinhua

    2008-01-01

    Three fully optimized geometries of 3-nitro-1,2,4-triazol-5-one-hydrogen fluoride (NTO-HF) complexes have been obtained with density functional theory (DFT) method at the B3LYP/6-311++G** level. The intermolecular interaction energy is calculated with zero point energy (ZPE) correction and basis set superposition error (BSSE) correction. The greatest corrected intermolecular interaction of the NTO-HF complexes is -34.155 kJ/mol. Electrons in complex systems transfer from NTO to HF. Natural bond orbital (NBO) analysis is performed to reveal the origin of the interaction. The strong hydrogen bonds contribute to the interaction energies dominantly. Frequency calculations are carried out on each optimized structure, and their IR spectra are discussed. Vibrational analysis show that there are large red-shifts for H-X (X = N and F) stretching vibrational frequencies in the NTO and hydrogen fluoride complexes. The changes of thermodynamic properties from the monomer to complexes with the temperature ranging from 200 K to 1500 K have been obtained using the statistical thermodynamic method. It is found that two of three NTO-HF complexes can be produced spontaneously from NTO and HF at room temperature

  20. DFT study of the interaction between 3-nitro-1,2,4-triazole-5-one and hydrogen fluoride

    Energy Technology Data Exchange (ETDEWEB)

    Fang Guoyong [College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035 (China); Xu Lina [College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035 (China)], E-mail: ahxulina@sohu.com; Hu Xingen; Li Xinhua [College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035 (China)

    2008-12-15

    Three fully optimized geometries of 3-nitro-1,2,4-triazol-5-one-hydrogen fluoride (NTO-HF) complexes have been obtained with density functional theory (DFT) method at the B3LYP/6-311++G** level. The intermolecular interaction energy is calculated with zero point energy (ZPE) correction and basis set superposition error (BSSE) correction. The greatest corrected intermolecular interaction of the NTO-HF complexes is -34.155 kJ/mol. Electrons in complex systems transfer from NTO to HF. Natural bond orbital (NBO) analysis is performed to reveal the origin of the interaction. The strong hydrogen bonds contribute to the interaction energies dominantly. Frequency calculations are carried out on each optimized structure, and their IR spectra are discussed. Vibrational analysis show that there are large red-shifts for H-X (X = N and F) stretching vibrational frequencies in the NTO and hydrogen fluoride complexes. The changes of thermodynamic properties from the monomer to complexes with the temperature ranging from 200 K to 1500 K have been obtained using the statistical thermodynamic method. It is found that two of three NTO-HF complexes can be produced spontaneously from NTO and HF at room temperature.

  1. Improved Interaction Potentials for Charged Residues in Proteins

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2008-01-01

    Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, exper......Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self......, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are ~2 kcal/mol with the new parameters, due to variations in system...

  2. Double folded Yukawa interaction potential between two heavy ions

    International Nuclear Information System (INIS)

    Bulgac, A.; Carstoiu, F.; Dumitrescu, O.

    1980-02-01

    A simple semi-analytical formula for the heavy ion interaction potential within the double-folding model approximation is obtained. The folded interaction is assumed to be expressed in Yukawa terms or the derivatives of them. The densities used can be both experimental or theoretical (of simple ''step-wise'', ''Fermi-Saxon-Woods'' or complicated ''shell model'' structure) densities. A way of inserting the exchange terms is discussed. Numerical calculations for some colliding partners are reported. (author)

  3. Clinically relevant potential drug-drug interactions among outpatients: A nationwide database study.

    Science.gov (United States)

    Jazbar, Janja; Locatelli, Igor; Horvat, Nejc; Kos, Mitja

    2018-06-01

    Adverse drug events due to drug-drug interactions (DDIs) represent a considerable public health burden, also in Slovenia. A better understanding of the most frequently occurring potential DDIs may enable safer pharmacotherapy and minimize drug-related problems. The aim of this study was to evaluate the prevalence and predictors of potential DDIs among outpatients in Slovenia. An analysis of potential DDIs was performed using health claims data on prescription drugs from a nationwide database. The Lexi-Interact Module was used as the reference source of interactions. The influence of patient-specific predictors on the risk of potential clinically relevant DDIs was evaluated using logistic regression model. The study population included 1,179,803 outpatients who received 15,811,979 prescriptions. The total number of potential DDI cases identified was 3,974,994, of which 15.6% were potentially clinically relevant. Altogether, 9.3% (N = 191,213) of the total population in Slovenia is exposed to clinically relevant potential DDIs, and the proportion is higher among women and the elderly. After adjustment for cofactors, higher number of medications and older age are associated with higher odds of clinically relevant potential DDIs. The burden of DDIs is highest with drug combinations that increase risk of bleeding, enhance CNS depression or anticholinergic effects or cause cardiovascular complications. The current study revealed that 1 in 10 individuals in the total Slovenian population is exposed to clinically relevant potential DDIs yearly. Taking into account the literature based conservative estimate that approximately 1% of potential DDIs result in negative health outcomes, roughly 1800 individuals in Slovenia experience an adverse health outcome each year as a result of clinically relevant potential interactions alone. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. The mechanism of interaction of polymethacrylic acid with sodium dodecylbenzenesulfonate in aqueous solutions

    Science.gov (United States)

    Sachko, A. V.; Zakordonskii, V. P.; Voloshinovskii, A. S.; Golod, T. Yu.

    2009-07-01

    A complex of physicochemical methods (light scattering, potentiometry, conductometry, viscometry, tensiometry, and fluorescence spectroscopy) were used to show the possibility of formation of intermolecular associates/complexes in systems with likely charged components. The driving forces of such interactions were analyzed and a possible scheme of complex formation between polymethacrylic acid and sodium dodecylbenzenesulfonate was suggested.

  5. Potential drug–drug interactions in Alzheimer patients with behavioral symptoms

    Directory of Open Access Journals (Sweden)

    Pasqualetti G

    2015-09-01

    Full Text Available Giuseppe Pasqualetti, Sara Tognini, Valeria Calsolaro, Antonio Polini, Fabio Monzani Geriatrics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy Abstract: The use of multi drug regimens among the elderly population has increased tremendously over the last decade although the benefits of medications are always accompanied by potential harm, even when prescribed at recommended doses. The elderly populations are particularly at an increased risk of adverse drug reactions considering comorbidity, poly-therapy, physiological changes affecting the pharmacokinetics and pharmacodynamics of many drugs and, in some cases, poor compliance due to cognitive impairment and/or depression. In this setting, drug–drug interaction may represent a serious and even life-threatening clinical condition. Moreover, the inability to distinguish drug-induced symptoms from a definitive medical diagnosis often results in addition of yet another drug to treat the symptoms, which in turn increases drug–drug interactions. Cognitive enhancers, including acetylcholinesterase inhibitors and memantine, are the most widely prescribed agents for Alzheimer’s disease (AD patients. Behavioral and psychological symptoms of dementia, including psychotic symptoms and behavioral disorders, represent noncognitive disturbances frequently observed in AD patients. Antipsychotic drugs are at high risk of adverse events, even at modest doses, and may interfere with the progression of cognitive impairment and interact with several drugs including anti-arrhythmics and acetylcholinesterase inhibitors. Other medications often used in AD patients are represented by anxiolytic, like benzodiazepine, or antidepressant agents. These agents also might interfere with other concomitant drugs through both pharmacokinetic and pharmacodynamic mechanisms. In this review we focus on the most frequent drug–drug interactions, potentially harmful, in AD patients with

  6. Expanding Interaction Potentials within Virtual Environments: Investigating the Usability of Speech and Manual Input Modes for Decoupled Interaction

    Directory of Open Access Journals (Sweden)

    Alex Stedmon

    2011-01-01

    Full Text Available Distributed technologies and ubiquitous computing now support users who may be detached or decoupled from traditional interactions. In order to investigate the potential usability of speech and manual input devices, an evaluation of speech input across different user groups and a usability assessment of independent-user and collaborative-user interactions was conducted. Whilst the primary focus was on a formative usability evaluation, the user group evaluation provided a formal basis to underpin the academic rigor of the exercise. The results illustrate that using a speech interface is important in understanding user acceptance of such technologies. From the usability assessment it was possible to translate interactions and make them compatible with innovative input devices. This approach to interaction is still at an early stage of development, and the potential or validity of this interfacing concept is still under evaluation; however, as a concept demonstrator, the results of these initial evaluations demonstrate the potential usability issues of both input devices as well as highlighting their suitability for advanced virtual applications.

  7. Vapour pressures of 1-methyl derivatives of benzimidazole, pyrazole and indole. The energy of the intermolecular hydrogen bond N-H⋯N

    International Nuclear Information System (INIS)

    Almeida, Ana R.R.P.; Monte, Manuel J.S.

    2014-01-01

    Highlights: • Vapour pressures of 1-methyl derivatives of benzimidazole, pyrazole and indole. • Enthalpies, entropies and Gibbs free energies of sublimation/vaporisation were derived. • Temperatures and enthalpies of fusion were determined. • Energy of the intermolecular hydrogen bond N-H⋯N was estimated. - Abstract: The vapour pressures of the liquid phase of 1-methylpyrazole, 1-methylbenzimidazole and 1-methylindole were measured over the temperature ranges (253.9 to 293.3) K, (303.2 to 372.5) K, and (268.6 to 341.9) K, respectively, using a static method. The vapour pressures of the crystalline phase of the two latter compounds were also measured at temperatures between (301.2 to 328.9) K and (267.6 to 275.5) K, respectively. The results obtained enabled the determination of the standard molar enthalpies and entropies of sublimation and of vaporisation at the mean temperatures of the measurements and at T = 298.15 K. The temperatures and molar enthalpies of fusion were determined using differential scanning calorimetry. The enthalpies of the intermolecular hydrogen bonds N-H⋯N in the crystalline phase of benzimidazole and pyrazole were determined and compared with the result previously determined for the energy of the intermolecular hydrogen bond in crystalline imidazole

  8. Perturbation theory of intermolecular interactions: What is the problem, are there solutions?

    International Nuclear Information System (INIS)

    Adams, W.H.

    1990-01-01

    We review the nature of the problem in the framework of Rayleigh-Schroedinger perturbation theory (the polarization approximation) considering explicitly two examples: the interaction of two hydrogen atoms and the interaction of Li with H. We show, in agreement with the work of Claverie and of Morgan and Simon, that the LiH problem is dramatically different from the H 2 problem. In particular, the physical states of LiH are higher in energy than an infinite number of discrete, unphysical states and they are buried in a continuum of unbound, unphysical states, which starts well below the lowest physical state. Clavrie has shown that the perturbation expansion, under these circumstances, is likely to converge to an unphysical state of lower energy than the physical ground state, if it converges at all. We review, also, the application of two classes of exchange perturbation theory to LiH and larger systems. We show that the spectra of three Eisenschitz-London (EL) class, exchange perturbation theories have no continuum of unphysical states overlaying the physical states and no discrete, unphysical states below the lowest physical state. In contrast, the spectra of two Hirschfelder-Silbey class theories differ hardly at all from that found with the polarization approximation. Not one of the EL class of perturbation theories, however, eliminates all of the discrete unphysical states

  9. Statistical analysis of simulation calculation of sputtering for two interaction potentials

    International Nuclear Information System (INIS)

    Shao Qiyun

    1992-01-01

    The effects of the interaction potentials (Moliere potential and Universal potential) are presented on computer simulation results of sputtering via Monte Carlo simulation based on the binary collision approximation. By means of Wilcoxon two-Sample paired sign rank test, the statistically significant difference for the above results is obtained

  10. Imaging molecular interaction of NO on Cu(110) with a scanning tunneling microscope.

    Science.gov (United States)

    Okuyama, Hiroshi

    2014-10-01

    Molecular interaction on metal surfaces is one of the central issues of surface science for the microscopic understanding of heterogeneous catalysis. In this Personal Account, I review the recent studies on NO/Cu(110) employing a scanning tunneling microscope (STM) to probe and control the molecule-molecule interaction on the surface. An individual NO molecule was observed as a characteristic dumbbell-shaped protrusion, visualizing the 2π* orbital. By manipulating the intermolecular distance with the STM, the overlap of the 2π* orbital between two NO molecules was controlled. The interaction causes the formation of the bonding and antibonding orbitals below and above the Fermi level, respectively, as a function of the intermolecular distance. The 2π* orbital also plays a role in the reaction of NO with water molecules. A water molecule donates a H-bond to NO, giving rise to the down-shift of the 2π* level below the Fermi level. This causes electron transfer from the substrate to NO, weakening, and eventually rupturing, the N-O bond. The facile bond cleavage by water molecules has implications for the catalytic reduction of NO under ambient conditions. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Choice of single-particle potential and the convergence of the effective interaction

    International Nuclear Information System (INIS)

    Hjorth-Jensen, M.; Osnes, E.; Muether, H.; Schmid, K.W.

    1990-02-01

    The convergence of the expansion for the effective interaction is studied considering as example the shell model for the nuclei 18 O and 18 F. In this work the effective interaction is computed through third order in the Brueckner G matrix, using both a harmonic-oscillator (HO) basis and a Brueckner-Hartree-Fock (BHF) basis. The significant differences in the convergence behavior of the effective interaction in these two cases are reported. The results indicate that the choice of the BHF single-particle potential facilitates the convergence of the effective interaction in low-orders of the expansion, whereas the HO results exhibit a non-convergent behavior. The implications for the HO approach are discussed. All calculations have been performed considering a modern version of the Bonn one-boson-exchange potential for the nucleon-nucleon interaction. 23 refs., 4 figs., 2 tabs

  12. Van der Waals potentials between metal clusters and helium atoms obtained with density functional theory and linear response methods

    International Nuclear Information System (INIS)

    Liebrecht, M.

    2014-01-01

    The importance of van der Waals interactions in many diverse research fields such as, e. g., polymer science, nano--materials, structural biology, surface science and condensed matter physics created a high demand for efficient and accurate methods that can describe van der Waals interactions from first principles. These methods should be able to deal with large and complex systems to predict functions and properties of materials that are technologically and biologically relevant. Van der Waals interactions arise due to quantum mechanical correlation effects and finding appropriate models an numerical techniques to describe this type of interaction is still an ongoing challenge in electronic structure and condensed matter theory. This thesis introduces a new variational approach to obtain intermolecular interaction potentials between clusters and helium atoms by means of density functional theory and linear response methods. It scales almost linearly with the number of electrons and can therefore be applied to much larger systems than standard quantum chemistry techniques. The main focus of this work is the development of an ab-initio method to account for London dispersion forces, which are purely attractive and dominate the interaction of non--polar atoms and molecules at large distances. (author) [de

  13. Exchange-Correlation Effects for Noncovalent Interactions in Density Functional Theory.

    Science.gov (United States)

    Otero-de-la-Roza, A; DiLabio, Gino A; Johnson, Erin R

    2016-07-12

    In this article, we develop an understanding of how errors from exchange-correlation functionals affect the modeling of noncovalent interactions in dispersion-corrected density-functional theory. Computed CCSD(T) reference binding energies for a collection of small-molecule clusters are decomposed via a molecular many-body expansion and are used to benchmark density-functional approximations, including the effect of semilocal approximation, exact-exchange admixture, and range separation. Three sources of error are identified. Repulsion error arises from the choice of semilocal functional approximation. This error affects intermolecular repulsions and is present in all n-body exchange-repulsion energies with a sign that alternates with the order n of the interaction. Delocalization error is independent of the choice of semilocal functional but does depend on the exact exchange fraction. Delocalization error misrepresents the induction energies, leading to overbinding in all induction n-body terms, and underestimates the electrostatic contribution to the 2-body energies. Deformation error affects only monomer relaxation (deformation) energies and behaves similarly to bond-dissociation energy errors. Delocalization and deformation errors affect systems with significant intermolecular orbital interactions (e.g., hydrogen- and halogen-bonded systems), whereas repulsion error is ubiquitous. Many-body errors from the underlying exchange-correlation functional greatly exceed in general the magnitude of the many-body dispersion energy term. A functional built to accurately model noncovalent interactions must contain a dispersion correction, semilocal exchange, and correlation components that minimize the repulsion error independently and must also incorporate exact exchange in such a way that delocalization error is absent.

  14. Effect of surface tension on the behavior of adhesive contact based on Lennard-Jones potential law

    Science.gov (United States)

    Zhu, Xinyao; Xu, Wei

    2018-02-01

    The present study explores the effect of surface tension on adhesive contact behavior where the adhesion is interpreted by long-range intermolecular forces. The adhesive contact is analyzed using the equivalent system of a rigid sphere and an elastic half space covered by a membrane with surface tension. The long-range intermolecular forces are modeled with the Lennard‒Jones (L‒J) potential law. The current adhesive contact issue can be represented by a nonlinear integral equation, which can be solved by Newton‒Raphson method. In contrast to previous studies which consider intermolecular forces as short-range, the present study reveals more details of the features of adhesive contact with surface tension, in terms of jump instabilities, pull-off forces, pressure distribution within the contact area, etc. The transition of the pull-off force is not only consistent with previous studies, but also presents some new interesting characteristics in the current situation.

  15. Ferromagnetic interactions in Ru(III)-nitronyl nitroxide radical complex: a potential 2p4d building block for molecular magnets.

    Science.gov (United States)

    Pointillart, Fabrice; Bernot, Kevin; Sorace, Lorenzo; Sessoli, Roberta; Gatteschi, Dante

    2007-07-07

    The reaction between [Ru(salen)(PPh3)Cl] and the 4-pyridyl-substituted nitronyl nitroxide radical (NITpPy) leads to the [Ru(salen)(PPh3)(NITpPy)](ClO4)(H2O)2 complex while the reaction with the azido anion (N3-) leads to the [Ru(salen)(PPh3)(N3)] complex 2 (where salen2- = N,N'-ethan-1,2-diylbis(salicylidenamine) and PPh3 = triphenylphosphine). Both compounds have been characterized by single crystal X-ray diffraction. The two crystal structures are composed by a [Ru(III)(salen)(PPh3)]+ unit where the Ru(III) ion is coordinated to a salen2- ligand and one PPh3 ligand in axial position. In 1 the Ru(III) ion is coordinated to the 4-pyridyl-substituted nitronyl nitroxide radical whereas in 2 the second axial position is occupied by the azido ligand. In both complexes the Ru(III) ions are in the same environment RuO2N3P, in a tetragonally elongated octhaedral geometry. The crystal packing of 1 reveals pi-stacking in pairs. While antiferromagnetic intermolecular interaction (J2 = 5.0 cm(-1)) dominates at low temperatures, ferromagnetic intramolecular interaction (J1 = -9.0 cm(-1)) have been found between the Ru(III) ion and the coordinated NITpPy.

  16. Inter- and intramolecular non-covalent interactions in 1-methylimidazole-2-carbaldehyde complexes of copper, silver, and gold

    Science.gov (United States)

    Koskinen, Laura; Jääskeläinen, Sirpa; Hirva, Pipsa; Haukka, Matti

    2014-09-01

    Three new imidazole compounds, [CuBr2(mimc)2] (1), [Ag(mimc)2][CF3SO3] (2), and [AuCl3(mimc)] (3) (mimc = 1-methylimidazole-2-carbaldehyde), have been synthesized, structurally characterized, and further analyzed using the QTAIM analysis. The compounds exhibit self-assembled 3D networks arising from intermolecular non-covalent interactions such as metallophilic interactions, metal-π contacts, halogens-halogen interactions, and hydrogen bonds. These weak interactions have a strong impact on the coordination sphere of the metal atoms and on the packing of compounds 1, 2, and 3.

  17. Interactions of ionic liquids and acetone: thermodynamic properties, quantum-chemical calculations, and NMR analysis.

    Science.gov (United States)

    Ruiz, Elia; Ferro, Victor R; Palomar, Jose; Ortega, Juan; Rodriguez, Juan Jose

    2013-06-20

    The interactions between ionic liquids (ILs) and acetone have been studied to obtain a further understanding of the behavior of their mixtures, which generally give place to an exothermic process, mutual miscibility, and negative deviation of Raoult's law. COSMO-RS was used as a suitable computational method to systematically analyze the excess enthalpy of IL-acetone systems (>300), in terms of the intermolecular interactions contributing to the mixture behavior. Spectroscopic and COSMO-RS results indicated that acetone, as a polar compound with strong hydrogen bond acceptor character, in most cases, establishes favorable hydrogen bonding with ILs. This interaction is strengthened by the presence of an acidic cation and an anion with dispersed charge and non-HB acceptor character in the IL. COSMO-RS predictions indicated that gas-liquid and vapor-liquid equilibrium data for IL-acetone systems can be finely tuned by the IL selection, that is, acting on the intermolecular interactions between the molecular and ionic species in the liquid phase. NMR measurements for IL-acetone mixtures at different concentrations were also carried out. Quantum-chemical calculations by using molecular clusters of acetone and IL species were finally performed. These results provided additional evidence of the main role played by hydrogen bonding in the behavior of systems containing ILs and HB acceptor compounds, such as acetone.

  18. Investigation on molecular interactions of antibiotics in alcohols using volumetric and acoustic studies at different temperatures

    International Nuclear Information System (INIS)

    Naseem, Bushra; Iftikhar, Madeeha

    2017-01-01

    Highlights: • Antibiotics in different alcohols are used to study their interactions in solutions. • Density and sound velocity for antibiotic solutions are measured at different temperatures. • Apparent molar volume and isentropic compressibility are used to calculate partial molar quantities. • Acoustical parameters are calculated and discussed in terms of solute–solute and solute–solvent interactions. - Abstract: The density and sound velocity for pure alcohols (methanol, ethanol, iso-propanol and n-butanol) and molal solutions of nitroimidazoles (metronidazole (MNZ) and dimetridazole (DMZ) have been measured at different temperatures (293.15–313.15 K). Different volumetric and acoustical parameters like apparent molar volume (V ϕ ), partial molar volume (VЛљ ϕ ), apparent molar isentropic compressibility (K ϕ ), partial molar isentropic compressibility (KЛљ ϕ ), hydration number (n H ), acoustic impedance (Z) and intermolecular free length (L f ) of antibiotic solutions were calculated from the experimental values of density and sound velocity. The derived values have been used to explore the solute–solute and solute–solvent interactions. The V ϕ values are positive and K ϕ values are negative in both antibiotics, indicative of strong solute–solvent interactions and closely packed structure of antibiotics in alcohols. The decreasing trend of L f with increasing antibiotic concentration shows the presence of strong intermolecular interactions in solutions.

  19. Exploration of the NH3-H2 van der Waals interaction by high level ab initio calculations

    International Nuclear Information System (INIS)

    Mladenovic, Mirjana; Lewerenz, Marius; Cilpa, Geraldine; Rosmus, Pavel; Chambaud, Gilberte

    2008-01-01

    The intermolecular potential energy for the van der Waals complex between ammonia and the hydrogen molecule has been studied by means of the coupled cluster CCSD(T) method and aug-cc-pVXZ (X = D, T, Q, 5) basis sets and with inclusion of the Boys and Bernardi counterpoise correction. For sufficiently large basis sets the only true electronic minimum energy structure of NH 3 -H 2 is found to possess C 3v point group symmetry. Various minimum energy paths for the relative motion of NH 3 and H 2 are analysed in order to understand the topography of the intermolecular potential. The complete basis set limit for the electronic dissociation energy is estimated to be about 253 cm -1 at the CCSD(T) level

  20. Quantum mechanical force field for water with explicit electronic polarization.

    Science.gov (United States)

    Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

    2013-08-07

    A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across

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

    Science.gov (United States)

    Morisawa, Yusuke; Suga, Arisa

    2018-05-01

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

  2. On modelling adiabatic N-soliton interactions and perturbations. Effects of external potentials

    International Nuclear Information System (INIS)

    Gerdjikov, V.; Baizakov, B.

    2005-01-01

    We analyze several perturbed versions of the complex Toda chain (CTC) in an attempt to describe the adiabatic N-soliton train interactions of the perturbed nonlinear Schrodinger equation (NLS). Particular types of perturbations, including quadratic and periodic external potentials are treated by both analytical and numerical means. We show that the perturbed CTC model provides a good description for the N-soliton interactions in the presence of a weak external potential. (authors)

  3. Towards first-principles based modeling of poly-3-alkylthiophenes: The nature of interactions in 2,2´-bithiophene dimer

    Czech Academy of Sciences Publication Activity Database

    Sitkiewicz, S. P.; Mikolajczyk, M. M.; Toman, Petr; Zalesny, R.; Bartkowiak, W.

    2013-01-01

    Roč. 566, 12 April (2013), s. 67-70 ISSN 0009-2614 R&D Projects: GA ČR(CZ) GAP205/10/2280 Grant - others:AV ČR(CZ) M200501204 Program:M Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : poly-3-alkylthiophenes * intermolecular interactions * interaction energy decomposition Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.991, year: 2013

  4. Electronic Mechanisms of Intra and Intermolecular J Couplings in Systems with C-H···O Interactions

    Directory of Open Access Journals (Sweden)

    Claudio N. Cavasotto

    2003-04-01

    Full Text Available Abstract: Correlation effects on the change of 1J(CH couplings in model systems I:NCH...H2O and II:CH4...H2O as a function of the H...O distance are discussed. RPA and SOPPA results follow a similar trend in system II. In system I RPA values decrease monotonously as the H...O distance decreases, while SOPPA ones exhibit flat maximum near equilibrium. Such different behavior is ascribed to the π-transmitted component. Intermolecular couplings at the equilibrium geometry of I are analyzed by means of the CLOPPA approach. The larger absolute value of 2hJ(CO compared to 1hJ(HO is found to arise from contributions involving a vacant LMO localized in the C-H...O moiety.

  5. Nucleon-nucleon interaction with quark exchanges and prediction to colour van der Waals potential

    International Nuclear Information System (INIS)

    Osman, A.

    1985-11-01

    The nucleon-nucleon interaction is considered by including the colour nucleon clusters. The nucleon-nucleon system is treated as a six-quark system. The obtained local potentials reduce the short-range repulsion. The resulted nucleon-nucleon potential by using a quark-quark potential well agrees with the central-force potentials. The phase shifts calculated by using these local potentials are in good agreement with those obtained from other methods. Introducing the quark-quark potential in the nucleon-nucleon interaction, leads to a colour van der Waals potential very strong compared with that predicted by experiments. (author)

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  7. Interaction between Al3+ and acrylic acid and polyacrylic acid in acidic aqueous solution: a model experiment for the behavior of Al3+ in acidified soil solution.

    Science.gov (United States)

    Etou, Mayumi; Masaki, Yuka; Tsuji, Yutaka; Saito, Tomoyuki; Bai, Shuqin; Nishida, Ikuko; Okaue, Yoshihiro; Yokoyama, Takushi

    2011-01-01

    From the viewpoint of the phytotoxicity and mobility of Al(3+) released from soil minerals due to soil acidification, the interaction between Al(3+) and acrylic acid (AA) and polyacrylic acid (PAA) as a model compound of fulvic acid was investigated. The interaction was examined at pH 3 so as to avoid the hydrolysis of Al(3+). The interaction between Al(3+) and AA was weak. However, the interaction between Al(3+) and PAA was strong and depended on the initial (COOH in PAA)/Al molar ratio (R(P)) of the solution. For the range of 1/R(P), the interaction between Al(3+) and PAA can be divided into three categories: (1) 1:1 Al-PAA-complex (an Al(3+) combines to a carboxyl group), (2) intermolecular Al-PAA-complex (an Al(3+) combines to more than 2 carboxyl groups of other Al-PAA-complexes) in addition to the 1:1 Al-PAA-complex and (3) precipitation of intermolecular complexes. In conclusion, R(P) is an important factor affecting the behavior of Al(3+) in acidic soil solution.

  8. A general approach to intermolecular carbonylation of arene C-H bonds to ketones through catalytic aroyl triflate formation

    Science.gov (United States)

    Garrison Kinney, R.; Tjutrins, Jevgenijs; Torres, Gerardo M.; Liu, Nina Jiabao; Kulkarni, Omkar; Arndtsen, Bruce A.

    2018-02-01

    The development of metal-catalysed methods to functionalize inert C-H bonds has become a dominant research theme in the past decade as an approach to efficient synthesis. However, the incorporation of carbon monoxide into such reactions to form valuable ketones has to date proved a challenge, despite its potential as a straightforward and green alternative to Friedel-Crafts reactions. Here we describe a new approach to palladium-catalysed C-H bond functionalization in which carbon monoxide is used to drive the generation of high-energy electrophiles. This offers a method to couple the useful features of metal-catalysed C-H functionalization (stable and available reagents) and electrophilic acylations (broad scope and selectivity), and synthesize ketones simply from aryl iodides, CO and arenes. Notably, the reaction proceeds in an intermolecular fashion, without directing groups and at very low palladium-catalyst loadings. Mechanistic studies show that the reaction proceeds through the catalytic build-up of potent aroyl triflate electrophiles.

  9. Interaction Potential between Parabolic Rotator and an Outside Particle

    Directory of Open Access Journals (Sweden)

    Dan Wang

    2014-01-01

    Full Text Available At micro/nanoscale, the interaction potential between parabolic rotator and a particle located outside the rotator is studied on the basis of the negative exponential pair potential 1/Rn between particles. Similar to two-dimensional curved surfaces, we confirm that the potential of the three-dimensional parabolic rotator and outside particle can also be expressed as a unified form of curvatures; that is, it can be written as the function of curvatures. Furthermore, we verify that the driving forces acting on the particle may be induced by the highly curved micro/nano-parabolic rotator. Curvatures and the gradient of curvatures are the essential elements forming the driving forces. Through the idealized numerical experiments, the accuracy of the curvature-based potential is preliminarily proved.

  10. Short range part of the NN interaction: Equivalent local potentials from quark exchange kernels

    International Nuclear Information System (INIS)

    Suzuk, Y.; Hecht, K.T.

    1983-01-01

    To focus on the nature of the short range part of the NN interaction, the intrinsically nonlocal interaction among the quark constituents of colorless nucleons is converted to an equivalent local potential using resonating group kernels which can be evaluated in analytic form. The WKB approximation based on the Wigner transform of the nonlocal kernels has been used to construct the equivalent potentials without recourse to the long range part of the NN interaction. The relative importance of the various components of the exchange kernels can be examined: The results indicate the importance of the color magnetic part of the exchange kernel for the repulsive part in the (ST) = (10), (01) channels, in particular since the energy dependence of the effective local potentials seems to be set by this term. Large cancellations of color Coulombic and quark confining contributions, together with the kinetic energy and norm exchange terms, indicate that the exact nature of the equivalent local potential may be sensitive to the details of the parametrization of the underlying quark-quark interaction. The equivalent local potentials show some of the characteristics of the phenomenological short range terms of the Paris potential

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

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  12. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

    Directory of Open Access Journals (Sweden)

    Fabiana A Caetano

    2015-12-01

    Full Text Available Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

  13. JCZS: An Intermolecular Potential Database for Performing Accurate Detonation and Expansion Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Baer, M.R.; Hobbs, M.L.; McGee, B.C.

    1998-11-03

    Exponential-13,6 (EXP-13,6) potential pammeters for 750 gases composed of 48 elements were determined and assembled in a database, referred to as the JCZS database, for use with the Jacobs Cowperthwaite Zwisler equation of state (JCZ3-EOS)~l) The EXP- 13,6 force constants were obtained by using literature values of Lennard-Jones (LJ) potential functions, by using corresponding states (CS) theory, by matching pure liquid shock Hugoniot data, and by using molecular volume to determine the approach radii with the well depth estimated from high-pressure isen- tropes. The JCZS database was used to accurately predict detonation velocity, pressure, and temperature for 50 dif- 3 Accurate predictions were also ferent explosives with initial densities ranging from 0.25 glcm3 to 1.97 g/cm . obtained for pure liquid shock Hugoniots, static properties of nitrogen, and gas detonations at high initial pressures.

  14. Effect of the van der Waals interaction on the electron energy-loss near edge structure theoretical calculation

    Energy Technology Data Exchange (ETDEWEB)

    Katsukura, Hirotaka; Miyata, Tomohiro; Tomita, Kota; Mizoguchi, Teruyasu, E-mail: teru@iis.u-tokyo.ac.jp

    2017-07-15

    The effect of the van der Waals (vdW) interaction on the simulation of the electron energy-loss near edge structure (ELNES) by a first-principles band-structure calculation is reported. The effect of the vdW interaction is considered by the Tkatchenko-Scheffler scheme, and the change of the spectrum profile and the energy shift are discussed. We perform calculations on systems in the solid, liquid and gaseous states. The transition energy shifts to lower energy by approximately 0.1 eV in the condensed (solid and liquid) systems by introducing the vdW effect into the calculation, whereas the energy shift in the gaseous models is negligible owing to the long intermolecular distance. We reveal that the vdW interaction exhibits a larger effect on the excited state than the ground state owing to the presence of an excited electron in the unoccupied band. Moreover, the vdW effect is found to depend on the local electron density and the molecular coordination. In addition, this study suggests that the detection of the vdW interactions exhibited within materials is possible by a very stable and high resolution observation. - Highlights: • Effect of van der Waals (vdW) interaction in ELNES calculation is investigated. • The vdW interaction influences more to the excited state owing to the presence of excited electron. • The vdW interaction makes spectral shift to lower energy side by 0.1–0.01 eV. • The vdW interaction is negligible in gaseous materials due to long intermolecular distance.

  15. Collisional effects on interaction potential in complex plasma in presence of magnetic field

    International Nuclear Information System (INIS)

    Bezbaruah, Pratikshya; Das, Nilakshi

    2016-01-01

    Interaction potential in complex plasma with streaming ions is derived analytically in presence of ion-neutral collision and magnetic field. The linear dielectric response function obtained describes the behavior of charged micron sized dust particles in strong collisional limit. A new type of repulsive potential is found to be operative among the dust grains apart from the normal Debye–Hückel potential. The amplitude and shielding length involved in the potential are substantially affected by the parameters describing ion cyclotron frequency, collision frequency among ions and neutrals, and ion streaming. It is also observed that the usual mechanism of ion focusing surrounding the grain is inhibited due to collision. As a result, the attractive wake potential structure is destroyed in the ion flow direction. The horizontal interaction involves only Debye–Hückel potential.

  16. Collisional effects on interaction potential in complex plasma in presence of magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Bezbaruah, Pratikshya, E-mail: pratphd@tezu.ernet.in; Das, Nilakshi [Department of Physics, Tezpur University, Tezpur, Assam 784028 (India)

    2016-04-15

    Interaction potential in complex plasma with streaming ions is derived analytically in presence of ion-neutral collision and magnetic field. The linear dielectric response function obtained describes the behavior of charged micron sized dust particles in strong collisional limit. A new type of repulsive potential is found to be operative among the dust grains apart from the normal Debye–Hückel potential. The amplitude and shielding length involved in the potential are substantially affected by the parameters describing ion cyclotron frequency, collision frequency among ions and neutrals, and ion streaming. It is also observed that the usual mechanism of ion focusing surrounding the grain is inhibited due to collision. As a result, the attractive wake potential structure is destroyed in the ion flow direction. The horizontal interaction involves only Debye–Hückel potential.

  17. Association of COMT and COMT-DRD2 interaction with creative potential

    Directory of Open Access Journals (Sweden)

    Shun eZhang

    2014-04-01

    Full Text Available Several lines of evidence suggest that genes involved in dopamine (DA transmission may contribute to creativity. Among these genes, the catechol-O-methyltransferase gene (COMT and the dopamine D2 receptor gene (DRD2 are the most promising candidates. Our previous study has revealed evidence for the involvement of DRD2 in creative potential. The present study extended our previous study by systematically exploring the association of COMT with creative potential as well as the interaction between COMT and DRD2. Twelve single nucleotide polymorphisms (SNPs covering COMT were genotyped in 543 healthy Chinese college students whose creative potentials were assessed by divergent thinking tests. Single SNP analysis showed that rs174697 was nominally associated with verbal originality, two SNPs (rs737865 and rs5993883 were nominally associated with figural fluency, and two SNPs (rs737865 and rs4680 were nominally associated with figural originality. Haplotype analysis showed that, the TCT and CCT haplotype (rs737865-rs174675-rs5993882 were nominally associated with figural originality, and the TATGCAG and CGCGGGA haplotype (rs4646312-rs6269-rs4633-rs6267-rs4818-rs4680-rs769224 were nominally associated with figural originality and verbal flexibility, respectively. However, none of these nominal findings survived correction for multiple testing. Gene-gene interaction analysis identified one significant four-way interaction of rs174675 (COMT, rs174697 (COMT, rs1076560 (DRD2 and rs4436578 (DRD2 on verbal fluency, one significant four-way interaction of rs174675 (COMT, rs4818 (COMT, rs1076560 (DRD2 and rs4648317 (DRD2 on verbal flexibility, and one significant three-way interaction of rs5993883 (COMT, rs4648319 (DRD2 and rs4648317 (DRD2 on figural flexibility. In conclusion, the present study provides nominal evidence for the involvement of COMT in creative potential and suggests that DA related genes may act in coordination to contribute to creativity.

  18. Spectral investigations and DFT studies of 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione (caffeine) interaction and recognition by single amino acid derived self-assembled nanostructures

    Science.gov (United States)

    Govindhan, R.; Karthikeyan, B.

    2018-03-01

    Recognition of xanthine alkaloid caffeine with 3,5-bis(trifluoromethyl)benzylamine derived peptide nanotubes (BTTPNTs) through chemical interaction have been achieved through the host-guest like interaction. DFT simulation is carried out for caffeine interacted with BTTPNTs system and also experimentally characterized by ultraviolet-visible (UV-vis) absorbance, confocal Raman spectra (CRS) with microscopic imaging (CRM), FT-Raman, surface enhanced Raman scattering (SERS), UV-diffuse reflectance spectra (UV-DRS), high resolution transmission electron microscopy (HR-TEM) and cyclic voltammetry (CV) studies. The results are used to examine the morphologies, size of the nanostructure and study of its interaction with the caffeine molecule. The results show that BTTPNTs is having potential for sensing the caffeine molecules through the binding occurred from the NH2 of tyrosine moiety of the BTTPNTs. This intermolecular association through face-to-face stacking of BTTPNTs is explained by detailed DFT calculations.

  19. Nucleon-nucleon interaction with quark exchange and prediction of the color van der Waals potential

    International Nuclear Information System (INIS)

    Osman, A.

    1988-01-01

    The nucleon-nucleon interaction is considered by including the color nucleon clusters. The nucleon-nucleon system is treated as a six-quark system. The obtained local potentials reduce the short-range repulsion. The resulting nucleon-nucleon potential, using a quark-quark potential, agress well with the central-force potentials. The phase shifts calculated by using these local potentials are in good agreement with those obtained from other methods. Introducing the quark-quark potential in the nucleon-nucleon interaction leads to a color van der Waals potential much stronger than that implied by experiments

  20. Nuclear interaction potential in a folded-Yukawa model with diffuse densities

    International Nuclear Information System (INIS)

    Randrup, J.

    1975-09-01

    The folded-Yukawa model for the nuclear interaction potential is generalized to diffuse density distributions which are generated by folding a Yukawa function into sharp generating distributions. The effect of a finite density diffuseness or of a finite interaction range is studied. The Proximity Formula corresponding to the generalized model is derived and numerical comparison is made with the exact results. (8 figures)

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  2. Prevalence of Potential and Clinically Relevant Statin-Drug Interactions in Frail and Robust Older Inpatients.

    Science.gov (United States)

    Thai, Michele; Hilmer, Sarah; Pearson, Sallie-Anne; Reeve, Emily; Gnjidic, Danijela

    2015-10-01

    A significant proportion of older people are prescribed statins and are also exposed to polypharmacy, placing them at increased risk of statin-drug interactions. To describe the prevalence rates of potential and clinically relevant statin-drug interactions in older inpatients according to frailty status. A cross-sectional study of patients aged ≥65 years who were prescribed a statin and were admitted to a teaching hospital between 30 July and 10 October 2014 in Sydney, Australia, was conducted. Data on socio-demographics, comorbidities and medications were collected using a standardized questionnaire. Potential statin-drug interactions were defined if listed in the Australian Medicines Handbook and three international drug information sources: the British National Formulary, Drug Interaction Facts and Drug-Reax(®). Clinically relevant statin-drug interactions were defined as interactions with the highest severity rating in at least two of the three international drug information sources. Frailty was assessed using the Reported Edmonton Frail Scale. A total of 180 participants were recruited (median age 78 years, interquartile range 14), 35.0% frail and 65.0% robust. Potential statin-drug interactions were identified in 10% of participants, 12.7% of frail participants and 8.5% of robust participants. Clinically relevant statin-drug interactions were identified in 7.8% of participants, 9.5% of frail participants and 6.8% of robust participants. Depending on the drug information source used, the prevalence rates of potential and clinically relevant statin-drug interactions ranged between 14.4 and 35.6% and between 14.4 and 20.6%, respectively. In our study of frail and robust older inpatients taking statins, the overall prevalence of potential statin-drug interactions was low and varied significantly according to the drug information source used.

  3. Potential intravenous drug interactions in intensive care.

    Science.gov (United States)

    Moreira, Maiara Benevides; Mesquita, Maria Gefé da Rosa; Stipp, Marluci Andrade Conceição; Paes, Graciele Oroski

    2017-07-20

    To analyze potential intravenous drug interactions, and their level of severity associated with the administration of these drugs based on the prescriptions of an intensive care unit. Quantitative study, with aretrospective exploratory design, and descriptive statistical analysis of the ICU prescriptions of a teaching hospital from March to June 2014. The sample consisted of 319 prescriptions and subsamples of 50 prescriptions. The mean number of drugs per patient was 9.3 records, and a higher probability of drug interaction inherent to polypharmacy was evidenced. The study identified severe drug interactions, such as concomitant administration of Tramadol with selective serotonin reuptake inhibitor drugs (e.g., Metoclopramide and Fluconazole), increasing the risk of seizures due to their epileptogenic actions, as well as the simultaneous use of Ranitidine-Fentanyl®, which can lead to respiratory depression. A previous mapping of prescriptions enables the characterization of the drug therapy, contributing to prevent potential drug interactions and their clinical consequences. Analisar as potenciais interações medicamentosas intravenosas e seu grau de severidade associadas à administração desses medicamentos a partir das prescrições do Centro de Terapia Intensiva. Estudo quantitativo, tipologia retrospectiva exploratória, com análise estatística descritiva das prescrições medicamentosas do Centro de Terapia Intensiva de um Hospital Universitário, no período de março-junho/2014. A amostra foi composta de 319 prescrições e subamostras de 50 prescrições. Constatou-se que a média de medicamentos por paciente foi de 9,3 registros, e evidenciou-se maior probabilidade para ocorrência de interação medicamentosa inerente à polifarmácia. O estudo identificou interações medicamentosas graves, como a administração concomitante de Tramadol com medicamentos inibidores seletivos da recaptação da serotonina, (exemplo: Metoclopramida e Fluconazol

  4. Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction.

    Science.gov (United States)

    Endoh, Tamaki; Sugimoto, Naoki

    2015-08-04

    Conformational transitions of biomolecules in response to specific stimuli control many biological processes. In natural functional RNA switches, often called riboswitches, a particular RNA structure that has a suppressive or facilitative effect on gene expression transitions to an alternative structure with the opposite effect upon binding of a specific metabolite to the aptamer region. Stability of RNA secondary structure (-ΔG°) can be predicted based on thermodynamic parameters and is easily tuned by changes in nucleobases. We envisioned that tuning of a functional RNA switch that causes an allosteric interaction between an RNA and a peptide would be possible based on a predicted switching energy (ΔΔG°) that corresponds to the energy difference between the RNA secondary structure before (-ΔG°before) and after (-ΔG°after) the RNA conformational transition. We first selected functional RNA switches responsive to neomycin with predicted ΔΔG° values ranging from 5.6 to 12.2 kcal mol(-1). We then demonstrated a simple strategy to rationally convert the functional RNA switch to switches responsive to natural metabolites thiamine pyrophosphate, S-adenosyl methionine, and adenine based on the predicted ΔΔG° values. The ΔΔG° values of the designed RNA switches proportionally correlated with interaction energy (ΔG°interaction) between the RNA and peptide, and we were able to tune the sensitivity of the RNA switches for the trigger molecule. The strategy demonstrated here will be generally applicable for construction of functional RNA switches and biosensors in which mechanisms are based on conformational transition of nucleic acids.

  5. NMR Detection of Semi-Specific Antibody Interactions in Serum Environments

    Directory of Open Access Journals (Sweden)

    Saeko Yanaka

    2017-09-01

    Full Text Available Although antibody functions are executed in heterogeneous blood streams characterized by molecular crowding and promiscuous intermolecular interaction, detailed structural characterizations of antibody interactions have thus far been performed under homogeneous in vitro conditions. NMR spectroscopy potentially has the ability to study protein structures in heterogeneous environments, assuming that the target protein can be labeled with NMR-active isotopes. Based on our successful development of isotope labeling of antibody glycoproteins, here we apply NMR spectroscopy to characterize antibody interactions in heterogeneous extracellular environments using mouse IgG-Fc as a test molecule. In human serum, many of the HSQC peaks originating from the Fc backbone exhibited attenuation in intensity of various magnitudes. Similar spectral changes were induced by the Fab fragment of polyclonal IgG isolated from the serum, but not by serum albumin, indicating that a subset of antibodies reactive with mouse IgG-Fc exists in human serum without preimmunization. The metaepitopes recognized by serum polyclonal IgG cover the entire molecular surface of Fc, including the binding sites to Fc receptors and C1q. In-serum NMR observation will offer useful tools for the detailed characterization of biopharamaceuticals, including therapeutic antibodies in physiologically relevant heterogeneous environments, also giving deeper insight into molecular recognition by polyclonal antibodies in the immune system.

  6. Study of Pair and many-body interactions in rare-gas halide atom clusters using negative ion zero electron kinetic energy (ZEKE) and threshold photodetachment spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Yourshaw, Ivan [Univ. of California, Berkeley, CA (United States)

    1998-07-09

    The diatomic halogen atom-rare gas diatomic complexes KrBr-, XeBr-, and KrCl- are studied in this work by zero electron kinetic energy (ZEKE) spectroscopy in order to characterize the weak intermolecular diatomic potentials of these species. Also, the ZEKE and threshold photodetachment spectra of the polyatomic clusters ArnBr- (n = 2-9) and ArnI- (n = 2-19) are studied to obtain information about the non-additive effects on the interactions among the atoms. This work is part of an ongoing effort to characterize the pair and many-body potentials of the complete series of rare gas halide clusters. In these studies we obtain information about both the anionic and neutral clusters.

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

    Science.gov (United States)

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

    2014-10-21

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

  8. Study of the validity of a combined potential model using the Hybrid Reverse Monte Carlo method in Fluoride glass system

    Directory of Open Access Journals (Sweden)

    M. Kotbi

    2013-03-01

    Full Text Available The choice of appropriate interaction models is among the major disadvantages of conventional methods such as Molecular Dynamics (MD and Monte Carlo (MC simulations. On the other hand, the so-called Reverse Monte Carlo (RMC method, based on experimental data, can be applied without any interatomic and/or intermolecular interactions. The RMC results are accompanied by artificial satellite peaks. To remedy this problem, we use an extension of the RMC algorithm, which introduces an energy penalty term into the acceptance criteria. This method is referred to as the Hybrid Reverse Monte Carlo (HRMC method. The idea of this paper is to test the validity of a combined potential model of coulomb and Lennard-Jones in a Fluoride glass system BaMnMF7 (M = Fe,V using HRMC method. The results show a good agreement between experimental and calculated characteristics, as well as a meaningful improvement in partial pair distribution functions (PDFs. We suggest that this model should be used in calculating the structural properties and in describing the average correlations between components of fluoride glass or a similar system. We also suggest that HRMC could be useful as a tool for testing the interaction potential models, as well as for conventional applications.

  9. Influence of Pauli principle and polarization on 16O + 16O interaction potential

    International Nuclear Information System (INIS)

    Nesterov, V.A.

    2012-01-01

    In the work have studied the dependence of the interaction potential on taking into account the Pauli principle as well as monopole and quadrupole polarization within approaches based on the energy-density formalism and two-center shell model wave functions for 16 O + 16 O system. In the adiabatic approximation it is shown that the contribution of the Pauli principle and polarization in colliding nuclei radically changes the behavior of interaction potential

  10. Effective interactions for valence-hole nuclei with modern meson-exchange potential models

    International Nuclear Information System (INIS)

    Hjort-Jensen, M.; Osnes, E.; Kuo, E.

    1991-10-01

    Within the framework of the folded-diagram theory, the authors have studied the effective interaction appropriate for hole-hole nuclei in the mass regions of 16 O and 40 Ca, using the Bonn and Paris potential models. To sum up the folded diagrams the renormalization procedure of Lee and Suzuki has been employed, using a so-called Q-box in which were included all one-body and two-body irreducible valence-linked diagrams through third order in perturbation theory. Discrepancies for the mass dependence of the effective interaction for several JT configurations with respect to empirically deduced mass dependencies is reported. The role of core polarization processes through third order were found to be one of the mechanisms behind these discrepancies. Compared to the results obtained with the Paris potential, more attraction is introduced by the Bonn potential for all matrix elements of concerns, a result which agrees well with previous findings for the particle-particle interaction in the same mass regions. A qualitative agreements with experimental data is obtained. 31 refs., 6 figs., 8 tabs

  11. Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Huang, Y.; Hobza, Pavel; Beran, G. J. O.

    2015-01-01

    Roč. 11, č. 7 (2015), s. 3065-3079 ISSN 1549-9618 R&D Projects: GA ČR GP13-01214P; GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : density functional theory * Plesset perturbation theory * noncovalent interactions * interaction energies Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.301, year: 2015

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

    Science.gov (United States)

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

    2013-09-01

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

  13. Potential drug-drug interactions with direct oral anticoagulants in elderly hospitalized patients.

    Science.gov (United States)

    Forbes, Heather L; Polasek, Thomas M

    2017-10-01

    To determine the prevalence and nature of potential drug-drug interactions (DDIs) with direct oral anticoagulants (DOACs) in elderly hospitalized patients. This was a retrospective observational study. Inclusion criteria were: aged over 65 years; taking apixaban, rivaroxaban or dabigatran; and admitted to the Repatriation General Hospital between April 2014 and July 2015. A list of clinically relevant 'perpetrator' drugs was compiled from product information, the Australian Medicines Handbook, the Australian National Prescribing Service resources, and local health network guidelines. The prevalence and nature of potential DDIs with DOACs was determined by comparing inpatient drug charts with the list of perpetrator drugs. There were 122 patients in the study with a mean age of 82 years. Most patients had nonvalvular atrial fibrillation and were taking DOACs to prevent thrombotic stroke (83%). Overall, 45 patients (37%) had a total of 54 potential DDIs. Thirty-five patients had potential pharmacodynamic DDIs with antidepressants, nonsteroidal anti-inflammatory drugs and antiplatelets (35/122, 29%). Nineteen patients had potential pharmacokinetic DDIs (19/122, 16%). Of these, 68% (13/19) were taking drugs that increase DOAC plasma concentrations (amiodarone, erythromycin, diltiazem or verapamil) and 32% (6/19) were taking drugs that decrease DOAC plasma concentrations (carbamazepine, primidone or phenytoin). There were no cases of patients taking contraindicated interacting drugs. Potential DDIs with DOACs in elderly hospital inpatients are relatively common, particularly interactions that may increase the risk of bleeding. The risk-benefit ratio of DOACs in elderly patients on polypharmacy should always be carefully considered.

  14. Temperature-dependent optical potential and mean free path based on Skyrme interactions

    International Nuclear Information System (INIS)

    Ge Lingxiao; Zhuo Yizhong; Noerenberg, W.; Technische Hochschule Darmstadt

    1986-03-01

    Optical potentials and mean free paths of nucleons at finite temperatures are studied by utilizing effective Skyrme interactions which yield 'good' optical potentials at zero temperature. The results for nuclear matter (symmetric and asymmetric) are applied within the local density approximation of finite nuclei at various temperatures. Because of the limitation due to zero-range forces used and the assumptions of temperature independent nuclear densities and effective Skyrme interactions made, the calculations are expected to be limited to nucleon energies between 10 and 50 MeV above the Fermi energy and to nuclear temperatures of less than 8 MeV. (orig.)

  15. An accurate method for the determination of unlike potential parameters from thermal diffusion data

    International Nuclear Information System (INIS)

    El-Geubeily, S.

    1997-01-01

    A new method is introduced by means of which the unlike intermolecular potential parameters can be determined from the experimental measurements of the thermal diffusion factor as a function of temperature. The method proved to be easy, accurate, and applicable two-, three-, and four-parameter potential functions whose collision integrals are available. The potential parameters computed by this method are found to provide a faith full representation of the thermal diffusion data under consideration. 3 figs., 4 tabs

  16. Mechanism of Intermolecular Electron Transfer in Bionanostructures

    Science.gov (United States)

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

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

  17. Accurate Intermolecular Interaction Energies from a Combination of MP2 and TDDFT Response Theory

    Czech Academy of Sciences Publication Activity Database

    Pitoňák, Michal; Hesselmann, A.

    2010-01-01

    Roč. 6, č. 1 (2010), s. 168-178 ISSN 1549-9618 R&D Projects: GA MŠk LC512 Grant - others:VEGA(SK) 1/0428/09 Institutional research plan: CEZ:AV0Z40550506 Keywords : dispersion energy * TDDFT * noncovalent interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.138, year: 2010

  18. Effect of molecular interactions on retention and selectivity in reversed-phase liquid chromatography.

    Science.gov (United States)

    Szepesy, László

    2002-06-25

    The linear solvation energy relationships (LSERs) have been applied in the last years for description and prediction of retention and selectivity in reversed-phase liquid chromatography with good results. Widely different stationary phases have been compared and characterized by LSERs. In recent publications the influence of the type of the organic moderator and the composition of the mobile phase have also been described. However, the influence of the molecular properties of the solutes to be separated has never been discussed. According to the LSER model variation in retention factors (log k) with solute structure can be related to their potential for various intermolecular interactions. The retention factor is given as the sum of the terms of the LSER equation representing various types of molecular interactions. For this reason the influence of the structure and molecular properties of the solutes to be separated can also be investigated using the LSER equation. In this study we shall demonstrate how the specific molecular interactions influence chromatographic retention and selectivity. We intend to show that retention and selectivity depend on all participants of the system. In addition to the structure and properties of the stationary phase and the type and composition of the mobile phase the molecular properties of the solutes, characterized by the solvation parameters, will also influence the type and extent of the various molecular interactions governing retention and selectivity.

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

    Directory of Open Access Journals (Sweden)

    Gajjela Raju

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

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

    Science.gov (United States)

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

    2012-01-01

    Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine hybrid (PBD1), mixed imine-amide pyrrolobenzodiazepine dimer (PBD2) and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) were studied. G-rich single-stranded oligonucleotide d(5′GGGGTTGGGG3′) designated as d(T2G8), from the telomeric region of Tetrahymena Glaucoma, was considered for the interaction with ligands. ESI-MS and spectroscopic methods viz., circular dichroism (CD), UV-Visible, and fluorescence were employed to investigate the G-quadruplex structures formed by d(T2G8) sequence and its interaction with PBD and TMPyP4 ligands. From ESI-MS spectra, it is evident that the majority of quadruplexes exist as d(T2G8)2 and d(T2G8)4 forms possessing two to ten cations in the centre, thereby stabilizing the complex. CD band of PBD1 and PBD2 showed hypo and hyperchromicity, on interaction with quadruplex DNA, indicating unfolding and stabilization of quadruplex DNA complex, respectively. UV-Visible and fluorescence experiments suggest that PBD1 bind externally where as PBD2 intercalate moderately and bind externally to G-quadruplex DNA. Further, melting experiments using SYBR Green indicate that PBD1 unfolds and PBD2 stabilizes the G-quadruplex complex. ITC experiments using d(T2G8) quadruplex with PBD ligands reveal that PBD1 and PBD2 prefer external/loop binding and external/intercalative binding to quadruplex DNA, respectively. From experimental results it is clear that the interaction of PBD2 and TMPyP4 impart higher stability to the quadruplex complex. PMID:22558271

  1. Serish inulin and wheat biopolymers interactions in model systems as a basis for understanding the impact of inulin on bread properties: a FTIR investigation.

    Science.gov (United States)

    Pourfarzad, Amir; Habibi Najafi, Mohammad B; Haddad Khodaparast, Mohammad H; Khayyat, Mohammad Hassanzadeh

    2015-12-01

    In this study the interactions between Serish root inulin and the main biopolymer types of wheat flour namely gluten, starch and phospholipid, were investigated in different model systems using Fourier transform infrared (FTIR) spectroscopy to unravel the underlying physical mechanism by which inulin impacts dough and bread properties. Interactions of inulin with starch and phospholipid were not considerable compared to gluten, but it was also clear that the modes of these interactions varied with the type and the amount of additives used in model formulation. This study revealed that when inulin is added to gluten, water redistribution promotes partial dehydration of gluten and collapse of β-spirals into intermolecular β-sheet structures; this trans-conformations might be due to physical reasons are believed to further impact the poor quality of bread containing added inulin. Upon performing Gaussian-Lorenzian curve fitting, it was observed that by adding of inulin to model systems, the relative contribution of characteristic peaks of β-turn and intramolecular β-sheet was progressively decreased whereas intermolecular β-sheet and α-helix contents were increased.

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

    Science.gov (United States)

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

    2015-08-01

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

  3. Potential of the neutron lloyd's mirror interferometer for the search for new interactions

    Energy Technology Data Exchange (ETDEWEB)

    Pokotilovski, Yu. N., E-mail: pokot@nf.jinr.ru [Joint Institute for Nuclear Research (Russian Federation)

    2013-04-15

    We discuss the potential of the neutron Lloyd's mirror interferometer in a search for new interactions at small scales. We consider three hypothetical interactions that may be tested using the interferometer. The chameleon scalar field proposed to solve the enigma of accelerating expansion of the Universe produces interaction between particles and matter. The axion-like spin-dependent coupling between a neutron and nuclei or/and electrons may result in a P- and T-noninvariant interaction with matter. Hypothetical non-Newtonian gravitational interactions mediates an additional short-range potential between neutrons and bulk matter. These interactions between the neutron and the mirror of a Lloyd-type neutron interferometer cause a phase shift of neutron waves. We estimate the sensitivity and systematic effects of possible experiments.

  4. The n→π* Interaction.

    Science.gov (United States)

    Newberry, Robert W; Raines, Ronald T

    2017-08-15

    The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group. Mixing of these orbitals releases energy, resulting in an attractive interaction. Hints of such interactions were evident in small-molecule crystal structures as early as the 1970s, but not until 2001 was the role of such interactions articulated clearly. These non-covalent interactions were first discovered during investigations into the thermostability of the proline-rich protein collagen, which achieves a robust structure despite a relatively low potential for hydrogen bonding. It was found that by modulating the distance between two carbonyl groups in the peptide backbone, one could alter the conformational preferences of a peptide bond to proline. Specifically, only the trans conformation of a peptide bond to proline allows for an attractive interaction with an adjacent carbonyl group, so when one increases the proximity of the two carbonyl groups, one enhances their interaction and promotes the trans conformation of the peptide bond, which increases the thermostability of collagen. More recently, attention has been paid to the nature of these interactions. Some have argued that rather than resulting from electron donation, carbonyl interactions are a particular example of dipolar interactions that are well-approximated by classical mechanics. However, experimental evidence has demonstrated otherwise. Numerous examples now exist where an increase in the dipole moment of a carbonyl group decreases the strength of its interactions with other carbonyl

  5. Constructing high-accuracy intermolecular potential energy surface with multi-dimension Morse/Long-Range model

    Science.gov (United States)

    Zhai, Yu; Li, Hui; Le Roy, Robert J.

    2018-04-01

    Spectroscopically accurate Potential Energy Surfaces (PESs) are fundamental for explaining and making predictions of the infrared and microwave spectra of van der Waals (vdW) complexes, and the model used for the potential energy function is critically important for providing accurate, robust and portable analytical PESs. The Morse/Long-Range (MLR) model has proved to be one of the most general, flexible and accurate one-dimensional (1D) model potentials, as it has physically meaningful parameters, is flexible, smooth and differentiable everywhere, to all orders and extrapolates sensibly at both long and short ranges. The Multi-Dimensional Morse/Long-Range (mdMLR) potential energy model described herein is based on that 1D MLR model, and has proved to be effective and accurate in the potentiology of various types of vdW complexes. In this paper, we review the current status of development of the mdMLR model and its application to vdW complexes. The future of the mdMLR model is also discussed. This review can serve as a tutorial for the construction of an mdMLR PES.

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

    Directory of Open Access Journals (Sweden)

    Xiu-Mei Mo

    2011-03-01

    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-hexafluoro-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 nanofibrous 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 β-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.

  7. PRESENTATION POTENTIAL USING IN PEDAGOGICAL INTERACTION PROCESS

    Directory of Open Access Journals (Sweden)

    Olga V. Ershova

    2016-01-01

    Full Text Available The given article is aimed at considering multimedia presentation potential and its influence on strengthening classroom teacher-student interaction. In the article the importance of using this kind of activity in the study process is pointed in connection with educational state policy on the one hand. On the other hand, gained students’ skills as a final result of work with presentations met employers’ demand for both parent and world labour-markets and bring competitive benefit to the candidates. Scientific novelty and results. Multimedia presentation is considered as a specific complex of classroom activities. The students are oriented on the self analysis and presentation assessment. It is shown that well-organized process of peer students’ assessment allows to simultaneously helping in solving the didactic and methodical problems. To this purpose the system of assessment criteria should be developed. It has to be clear for students for making assessment feasible and time-saving. The example of a possible variant of criteria system is described; quality of the presentations prepared by students can be defined based on such system criteria. The author also analyzed software products of the three main platforms (Windows, Linux, MacOs which have different tools and allow to follow users’ needs for creating presentations. In the article there is a comparative table of the two most popular software development: the program Microsoft PowerPoint and the web-service Prezi for realizing the relevance of their use in the study process. Practical significance of the present article concludes in author’s suggestions of some recommendations for presentation potential use as a tool of improving pedagogical interaction process with contemporary students. 

  8. Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Richter, Andreas S.; Gorodkin, Jan

    2010-01-01

    of that used for individual multiple alignments. Results: We derived a rather extensive algorithm. One of the advantages of our approach (in contrast to other RNARNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra- and inter-molecular base...... pairs. As a proof of concept, we show an example and discuss the strengths and weaknesses of the approach....

  9. Interaction potential and repulsive force between atoms whose internuclear separations are small

    International Nuclear Information System (INIS)

    Barbaro, Jacques

    1971-01-01

    The Thomas-Fermi equation is solved for the homonuclear diatomic molecule. The electronic density and electrostatic potential at each point are used to calculate energies and interaction potentials for very small internuclear separation distances. The repulsive force between atoms is derived by means of the virial theorem. (author) [fr

  10. Non-potential interactions and the origin of masses of elementary particles

    International Nuclear Information System (INIS)

    Sun, J.

    1982-01-01

    We propose a fundamental assumption on internal states of particles. It follows from the fundamental assumption that: (1) the constituents of particles become non-particle objects; and (2) there appear naturally non-potential interactions. This non-potential interaction leads to a series of interesting results, one of which is that it yields the origin of masses of elementary particles. All mass values are given by the theory without pre-assumed mass values of the constituents (except the rest mass of the electron; mass is a physical quantity which appears only in particles but not in their constituents). The theoretically calculated mass values are in excellent agreement with the experimental values. In all calculations, only one constant b = 0.99935867 is introduced (bc being the speed of internal motion)

  11. Monte Carlo study of one-dimensional confined fluids with Gay-Berne intermolecular potential

    Science.gov (United States)

    Moradi, M.; Hashemi, S.

    2011-11-01

    The thermodynamic quantities of a one dimensional system of particles with Gay-Berne model potential confined between walls have been obtained by means of Monte Carlo computer simulations. For a number of temperatures, the systems were considered and their density profiles, order parameter, pressure, configurational temperature and average potential energy per particle are reported. The results show that by decreasing the temperature, the soft particles become more ordered and they align to the walls and also they don't show any tendency to be near the walls at very low temperatures. We have also changed the structure of the walls by embedding soft ellipses in them, this change increases the total density near the wall whereas, increasing or decreasing the order parameter depend on the angle of embedded ellipses.

  12. Accuracy of Several Wave Function and Density Functional Theory Methods for Description of Noncovalent Interaction of Saturated and Unsaturated Hydrocarbon Dimers

    Czech Academy of Sciences Publication Activity Database

    Granatier, Jaroslav; Pitoňák, M.; Hobza, Pavel

    2012-01-01

    Roč. 8, č. 7 (2012), s. 2282-2292 ISSN 1549-9618 Grant - others:APVV(SK) APVV-0059-10 Institutional research plan: CEZ:AV0Z40550506 Keywords : intermolecular interaction energies * Plesset perturbation-theory * molecular-orbital methods * protein rubredoxin Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.389, year: 2012

  13. Theoretical Studies of Solid Nitromethane

    National Research Council Canada - National Science Library

    Sorescu, Dan

    2001-01-01

    .... The intermolecular potential used is of the Buckingham 6-exp form plus charge-charge Coulombic interactions and has been previously developed by us (Sorescu, D. C.; Rice, B. M.; Thompson, D. L. J: Phys. Chem. 1997, BlOl, 798...

  14. Resonance Raman spectra of organic molecules absorbed on inorganic semiconducting surfaces: Contribution from both localized intramolecular excitation and intermolecular charge transfer excitation

    International Nuclear Information System (INIS)

    Ye, ChuanXiang; Zhao, Yi; Liang, WanZhen

    2015-01-01

    The time-dependent correlation function approach for the calculations of absorption and resonance Raman spectra (RRS) of organic molecules absorbed on semiconductor surfaces [Y. Zhao and W. Z. Liang, J. Chem. Phys. 135, 044108 (2011)] is extended to include the contribution of the intermolecular charge transfer (CT) excitation from the absorbers to the semiconducting nanoparticles. The results demonstrate that the bidirectionally interfacial CT significantly modifies the spectral line shapes. Although the intermolecular CT excitation makes the absorption spectra red shift slightly, it essentially changes the relative intensities of mode-specific RRS and causes the oscillation behavior of surface enhanced Raman spectra with respect to interfacial electronic couplings. Furthermore, the constructive and destructive interferences of RRS from the localized molecular excitation and CT excitation are observed with respect to the electronic coupling and the bottom position of conductor band. The interferences are determined by both excitation pathways and bidirectionally interfacial CT

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-10-28

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

  16. Study of various models of nuclear interaction potentials: nucleon-nucleus and nucleus-nucleus systems

    International Nuclear Information System (INIS)

    Ngo, H.

    1984-01-01

    Several models, performed within a mean field theory, are developed for the calculation of nucleon-nucleus interaction potentials. The first part of the thesis deals with the nucleon-nucleus average interaction. It is mainly devoted to the calculation of dynamical corrections to the Hartree-Fock approximation. Two approaches are used: a microscopic model performed in the framework of the nuclear structure approach and a semi-phenomenological one, based on the application of the dispersion relations to the empirical imaginary potential. Both models take into account finite size effects like collectivity or threshold effects which are important at low energy. The Green's function properties are used for both models. The second part of this work is devoted to the interaction potential between two heavy ions. This calculation, which is performed in the framework of the sudden approximation, uses the energy density formalism (Thomas-Fermi approximation). It has been extended to finite temperature. At T=0 the experimental fusion barriers of heavy systems are reproduced within 4%. Their temperature dependence is studied. The proximity scaling is checked and a universal function is obtained at T=0 and at finite temperature. It is found that the proximity theorem is well satisfied on the average. The dispersion around the mean behaviour increases with increasing temperature. At last, P+A* and α+A* interaction potentials are calculated within a double folding model using a schematic effective interaction [fr

  17. The weak π − π interaction originated resonant tunneling and fast switching in the carbon based electronic devices

    Directory of Open Access Journals (Sweden)

    Jun He

    2012-03-01

    Full Text Available By means of the nonequilibrium Green's functions and the density functional theory, we have investigated the electronic transport properties of C60 based electronic device with different intermolecular interactions. It is found that the electronic transport properties vary with the types of the interaction between two C60 molecules. A fast electrical switching behavior based on negative differential resistance has been found when two molecules are coupled by the weak π − π interaction. Compared to the solid bonding, the weak interaction is found to induce resonant tunneling, which is responsible for the fast response to the applied electric field and hence the velocity of switching.

  18. The Odd Power of Dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Peng [Iowa State Univ., Ames, IA (United States)

    2014-12-01

    In ancient China, water has been regarded as one of the five vital components of life. It has been observed that water has many fascinating properties: water is ‘soft’ yet it can penetrate a hard rock; water is ‘pure’ yet it can tolerate other beings. Because of its unique properties, water is often associated with good quality and has been given the highest praise by Laozi in his book Tao Te Ching saying: the highest/best quality that one can have is being like water. However, little did people understand why and how water possesses such fascinating properties. Modern scientific developments made people realize that the macroscopic liquid water is made of a large number of water molecules held together via a network of hydrogen bonds. And those wonderful properties of water are merely the macroscopic manifestations of the interactions between water molecules and other molecules. For example, the dissolving ability of water is due to the fact that the interaction between a water molecule and the other molecular species is stronger than the interactions among their own molecular species. In fact the interactions between any two molecules are governed by the same physics and are termed intermolecular interaction (or intermolecular forces in some literature, although technically ‘force’ is incorrect usage here). Although the very existence of the intermolecular interactions is easily proved, e.g. the mere presence of the solid phase of matter, and scientists today have recognized that the seemingly weak intermolecular interactions essentially hold the world together through a delicate and cooperative process, the theoretical understanding of various intermolecular interactions is still far from satisfactory. On the practical side, theoreticians need to balance computational cost and accuracy. Because of the relatively small magnitudes of the intermolecular interactions, errors that appear tiny compared to the usual chemical (covalent) bonding may change

  19. Hulthén and Coulomb-Like Potentials as a Tensor Interaction within the Relativistic Symmetries of the Manning-Rosen Potential

    International Nuclear Information System (INIS)

    Tokmehdashi, Hadi; Rajabi, Ali Akbar; Hamzavi, Majid

    2014-01-01

    The bound-state solutions of the Dirac equation for the Manning-Rosen potential are presented approximately for arbitrary spin-orbit quantum number κ with the Hulthén and Coulomb-like potentials as a tensor interaction. The generalized parametric Nikiforov-Uvarov (NU) method is used to obtain energy eigenvalues and corresponding two-component spinors of the two Dirac particles and these are obtained in the closed form by using the framework of the spin symmetry and p-spin symmetry concept. We have also shown that tensor interaction removes degeneracies between spin and p-spin doublets. Some numerical results are also given

  20. Cosmological solutions in string theory with dilaton self interaction potential

    International Nuclear Information System (INIS)

    Mora, C.; Pimentel, L.O.

    2003-01-01

    In this work we present homogeneous and isotropic cosmological solutions for the low energy limit of string theory with a self interacting potential for the scalar field. For a potential that is a linear combination of two exponential, a family of exact solutions are found for the different spatial curvatures. Among this family a non singular accelerating solution for positive curvature is singled out and the violation of the energy conditions for that solution is studied, and also its astrophysical consequences. The string coupling for this solution is finite. (Author)

  1. Potential drug-drug and drug-disease interactions in well-functioning community-dwelling older adults.

    Science.gov (United States)

    Hanlon, J T; Perera, S; Newman, A B; Thorpe, J M; Donohue, J M; Simonsick, E M; Shorr, R I; Bauer, D C; Marcum, Z A

    2017-04-01

    There are few studies examining both drug-drug and drug-disease interactions in older adults. Therefore, the objective of this study was to describe the prevalence of potential drug-drug and drug-disease interactions and associated factors in community-dwelling older adults. This cross-sectional study included 3055 adults aged 70-79 without mobility limitations at their baseline visit in the Health Aging and Body Composition Study conducted in the communities of Pittsburgh PA and Memphis TN, USA. The outcome factors were potential drug-drug and drug-disease interactions as per the application of explicit criteria drawn from a number of sources to self-reported prescription and non-prescription medication use. Over one-third of participants had at least one type of interaction. Approximately one quarter (25·1%) had evidence of had one or more drug-drug interactions. Nearly 10·7% of the participants had a drug-drug interaction that involved a non-prescription medication. % The most common drug-drug interaction was non-steroidal anti-inflammatory drugs (NSAIDs) affecting antihypertensives. Additionally, 16·0% had a potential drug-disease interaction with 3·7% participants having one involving non-prescription medications. The most common drug-disease interaction was aspirin/NSAID use in those with history of peptic ulcer disease without gastroprotection. Over one-third (34·0%) had at least one type of drug interaction. Each prescription medication increased the odds of having at least one type of drug interaction by 35-40% [drug-drug interaction adjusted odds ratio (AOR) = 1·35, 95% confidence interval (CI) = 1·27-1·42; drug-disease interaction AOR = 1·30; CI = 1·21-1·40; and both AOR = 1·45; CI = 1·34-1·57]. A prior hospitalization increased the odds of having at least one type of drug interaction by 49-84% compared with those not hospitalized (drug-drug interaction AOR = 1·49, 95% CI = 1·11-2·01; drug-disease interaction AOR = 1·69, CI = 1·15-2

  2. Scattering at low energies by potentials containing power-law corrections to the Coulomb interaction

    International Nuclear Information System (INIS)

    Kuitsinskii, A.A.

    1986-01-01

    The low-energy asymptotic behavior is found for the phase shifts and scattering amplitudes in the case of central potentials which decrease at infinity as n/r+ar /sup -a/,a 1. In problems of atomic and nuclear physics one is generally interested in collisions of clusters consisting of several charged particles. The effective interaction potential of such clusters contains long-range power law corrections to the Coulomb interaction that is presented

  3. Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases

    Energy Technology Data Exchange (ETDEWEB)

    Bartocci, Alessio; Cappelletti, David; Pirani, Fernando [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia 06123 (Italy); Belpassi, Leonardo [Istituto di Scienze e Tecnologie Molecolari del CNR, Perugia 06123 (Italy); Falcinelli, Stefano [Dipartimento di Ingegneria Civile ed Ambientale, Università degli Studi di Perugia, 06125 Perugia (Italy); Grandinetti, Felice [Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, 01100 Viterbo (Italy); Tarantelli, Francesco [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia 06123 (Italy); Istituto di Scienze e Tecnologie Molecolari del CNR, Perugia 06123 (Italy)

    2015-05-14

    The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl{sub 4} and CF{sub 4}. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypical Ng-CCl{sub 4} and Ng-CF{sub 4} and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF{sub 4}, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl{sub 4}, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential

  4. Optical potentials derived from microscopic separable interactions including binding and recoil effects

    International Nuclear Information System (INIS)

    Siciliano, E.R.; Walker, G.E.

    1976-01-01

    We first consider a projectile scattering from a nucleon bound in a fixed potential. A separable Galilean invariant projectile-nucleon interaction is adopted. Without using the fixed scatterer approximation or using closure on the intermediate target nucleon states we obtain various forms for the projectile-bound nucleon t matrix. Effects due to intermediate target excitation and nucleon recoil are discussed. By making the further approximations of closure and fixed scatterers we make connection with the work of previous authors. By generalizing to projectile interaction with several bound nucleons and examining the appropriate multiple scattering series we identify the optical potential for projectile elastic scattering from the many-body system. Different optical potentials are obtained for different projectile-bound nucleon t matrices, and we study the differences predicted by these dissimilar optical potentials for elastic scattering. In a model problem, we study pion-nucleus elastic scattering and compare the predictions obtained by adopting procedures used by (1) Landau, Phatak, and Tabakin and (2) Piepho-Walker to the predictions obtained in a less restrictive, but computationally difficult treatment

  5. Nematic-isotropic transition in some lattice models for rigid cores having semiflexible tails: segmental Lennard-Jones interactions

    International Nuclear Information System (INIS)

    Dowell, F.

    1983-01-01

    Two average-environment simple cubic lattice models: a refined model and a simple model, both having site-site (segmental) pair Lennard-Jones (LJ) interactions: for molecules composed of rigid cores having semiflexible tails are presented. The calculated values of the following properties at the nematic-isotropic transition for rigid rods of varying length are compared with relevant experimental data for PAA (p-azoxyanisole, or 4,4'-dimethoxyazoxybenzene): temperature, core orientational order parameter, nematic density and volume, relative density change, and relative entropy change. The temperature change as a function of volume change at constant order parameter is also discussed. In general, both LJ models give considerably better quantitative agreement with experiment, especially for the temperature and the relative density change, than do the earlier lattice models with hard repulsions, with or without constant segmental pair interaction energies. In most aspects, these LJ models give good quantitative agreement with experiment. These LJ models elucidate the importance of realistic intermolecular potentials, especially the role of soft repulsions, in describing an order-disorder transition between two condensed phases

  6. Intermolecular potential for Ar + D2O from differential scattering cross sections, and its implications for the water pair potential

    International Nuclear Information System (INIS)

    Brooks, R.; Porter, R.A.R.; Kalos, F.; Grosser, A.E.

    1975-01-01

    A velocity selected molecular beam of D 2 O was crossed with a nozzle beam of Ar and the angular distribution of the scattered D 2 O was measured mass spectrometrically. By varying the velocity of the D 2 O beam, the differential cross section was measured at two collision energies. The experimental results were compared with synthetic differential cross sections calculated from Lennard-Jones and Kihara-Stockmayer trial potentials to determine potential parameters. Implications for the H 2 O pair potential are discussed

  7. Synthesis of biological active thiosemicarbazone and characterization of the interaction with human serum albumin

    International Nuclear Information System (INIS)

    Yu, Wangshu; Shi, Lei; Hui, Guangquan; Cui, Fengling

    2013-01-01

    The synthesis of a new biological active reagent, 2-((1,4-dihydroxy)-9,10-anthraquinone) aldehyde thiosemicarbazone (DHAQTS), was designed. The interaction between DHAQTS and HSA was studied by fluorescence spectroscopy in combination with molecular modeling under simulation of physiological conditions. According to the results of fluorescence measurements, the quenching mechanism was suggested to be static. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrophobic interactions are the predominant intermolecular forces stabilizing the complex. The number of binding sites (n) was calculated. Through the site marker competitive experiment, DHAQTS was confirmed to be located in site I of HSA. The binding distance r=2.83 nm between the donor HSA and acceptor DHAQTS was obtained according to Förster's non-radiative energy transfer theory. The three-dimensional fluorescence spectral results showed the conformation and microenvironment of HSA changed in the presence of DHAQTS. The effects of common ions on the binding of DHAQTS to HSA were also evaluated. The experimental results were in agreement with the results obtained via a molecular docking study. - Highlights: ► 2-((1,4-dihydroxy)-9,10-anthraquinone)aldehyde thiosemicarbazone (DHAQTS) was synthesized. ► DHAQTS can quench the fluorescence of human serum albumin (HSA) by static quenching mechanism. ► Hydrophobic interactions were the predominant intermolecular forces. ► The competitive experiment was carried out to identify the DHAQTS binding site on HSA. ► Three-dimensional spectra confirmed DHAQTS caused the conformational change of HSA.

  8. Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

    OpenAIRE

    Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

    2002-01-01

    The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in ...

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

    CERN Document Server

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

    2003-01-01

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

  10. Empirical temperature-dependent intermolecular potentials determined by data mining from crystal data

    Science.gov (United States)

    Hofmann, D. W. M.; Kuleshova, L. N.

    2018-05-01

    Modern force fields are accurate enough to describe thermal effects in molecular crystals. Here, we have extended our earlier approach to discrete force fields for various temperatures to a force field with a continuous function. For the parametrisation of the force field, we used data mining on experimental structures with the temperature as an additional descriptor. The obtained force field can be used to minimise energy at a finite temperature and for molecular dynamics with zero-K potentials. The applicability of the method has been demonstrated for the prediction of crystal density, temperature density gradients and transition temperature.

  11. PICK1 interacts with ABP/GRIP to regulate AMPA receptor trafficking.

    Science.gov (United States)

    Lu, Wei; Ziff, Edward B

    2005-08-04

    PICK1 and ABP/GRIP bind to the AMPA receptor (AMPAR) GluR2 subunit C terminus. Transfer of the receptor from ABP/GRIP to PICK1, facilitated by GluR2 S880 phosphorylation, may initiate receptor trafficking. Here we report protein interactions that regulate these steps. The PICK1 BAR domain interacts intermolecularly with the ABP/GRIP linker II region and intramolecularly with the PICK1 PDZ domain. Binding of PKCalpha or GluR2 to the PICK1 PDZ domain disrupts the intramolecular interaction and facilitates the PICK1 BAR domain association with ABP/GRIP. Interference with the PICK1-ABP/GRIP interaction impairs S880 phosphorylation of GluR2 by PKC and decreases the constitutive surface expression of GluR2, the NMDA-induced endocytosis of GluR2, and recycling of internalized GluR2. We suggest that the PICK1 interaction with ABP/GRIP is a critical step in controlling GluR2 trafficking.

  12. Solid phase stability of a double-minimum interaction potential system

    International Nuclear Information System (INIS)

    Suematsu, Ayumi; Yoshimori, Akira; Saiki, Masafumi; Matsui, Jun; Odagaki, Takashi

    2014-01-01

    We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function

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

    Science.gov (United States)

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

    2013-01-15

    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 (ωB97X, ωB97, LC-ωPBE, 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, ωB97X-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 ωB97X-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, ωB97X-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. Copyright © 2012 Wiley Periodicals, Inc.

  14. Iron(II)-catalyzed intermolecular amino-oxygenation of olefins through the N-O bond cleavage of functionalized hydroxylamines.

    Science.gov (United States)

    Lu, Deng-Fu; Zhu, Cheng-Liang; Jia, Zhen-Xin; Xu, Hao

    2014-09-24

    An iron-catalyzed diastereoselective intermolecular olefin amino-oxygenation reaction is reported, which proceeds via an iron-nitrenoid generated by the N-O bond cleavage of a functionalized hydroxylamine. In this reaction, a bench-stable hydroxylamine derivative is used as the amination reagent and oxidant. This method tolerates a range of synthetically valuable substrates that have been all incompatible with existing amino-oxygenation methods. It can also provide amino alcohol derivatives with regio- and stereochemical arrays complementary to known amino-oxygenation methods.

  15. [Noncovalent cation-π interactions--their role in nature].

    Science.gov (United States)

    Fink, Krzysztof; Boratyński, Janusz

    2014-11-07

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

  16. Analysis of vibronic interactions in the molecules of cross-conjugated ketones

    Directory of Open Access Journals (Sweden)

    Kompaneez V.V.

    2017-01-01

    Full Text Available We have done quantitative analysis of vibronic parameters of two cross-conjugated δ-dimethylaminoketones. The research shows the influence of С-N and C=O bonds in the rings, and the radicals with nitro compounds on the vibronic parameters of characteristic bands, which describe the state (vibrations, types of deformation under excitation of the phenyl ring and the polyene bridge. Results described impact of the substituent’s nature on the parameters of intra- and intermolecular interactions presents for the studied compounds.

  17. Prevalence and typology of potential drug interactions occurring in primary care patients.

    Science.gov (United States)

    Lopez-Picazo, Julio J; Ruiz, Juan C; Sanchez, Jose F; Ariza, Angeles; Aguilera, Belen; Lazaro, Dolores; Sanz, Gonzalo R

    2010-06-01

    To investigate the prevalence and types of potential drug interactions in primary care patients to detect risky prescriptions as an essential condition to design intervention policies leading to an improvement in patient safety. Cross-sectional descriptive study. Two areas in Spain comprising 715,661 inhabitants. 430,525 subjects with electronic medical records and assigned to a family doctor regularly updating them. On a random day, 29.4% of the population was taking medication. Of these, 73.9% were at risk of suffering interactions, and these were found in 20.6% of them. The amount of interactions was higher among people with chronic conditions, the elderly, females and polymedicated patients. From the total of interactions, 55.1% belonged to the highest clinical relevance 'A' level, and 28.3% should have been avoided. The active ingredients primarily involved were hydrochlorothiazide and ibuprofen and, when focusing on those that should be avoided, omeprazole and acenocoumarol. The most frequent 'A' interaction that should be avoided was between non-conjugated excreted benzodiazepines and proton-pump inhibitors, followed by some NSAIDs and diuretics. 1 in 20 Spanish citizens is currently undergoing a potential drug interaction, including a high rate of clinically relevant ones that should be avoided. These results confirm the existence of a serious safety issue that should be approached and where all parties involved (physicians, health services, medical societies and patients) must do our bit to improve. Health services should foster the implementation of prescription alert systems linked with electronic medical records including clinical data.

  18. Van der Waals bond in dimers: H2Ne, H2Ar, H2Kr

    International Nuclear Information System (INIS)

    Waaijer, M.

    1981-01-01

    The H 2 -inert gas dimers H 2 X, and particularly H 2 Ne, H 2 Ar and H 2 Kr, form the subject of this thesis and are loosely bound van der Waals complexes, which is reflected in the low number of bound states and the small anisotropic interaction. The H 2 X dimers studied are formed in a supersonic nozzle expansion, in which the internal energy is converted into the macroscopic flow energy, establishing an internal temperature drop to 3 K, which favours dimer formation. Because of this cooling the H 2 X dimers relax to the lowest rotational states. The hyperfine transitions have been measured using magnetic beam resonance and yield information about the isotropic as well as the anisotropic intermolecular potential in the range between the classical turning points and in the adjacent part of the repulsive branch. The sensitivity of the method is very high and slight changes in the intermolecular potential cause significant effects. The analysis of the measured hyperfine transitions incorporates all interacting states of the molecule, bound as well as unbound (continuum) states. For H 2 Ne, which is the best studied H 2 -inert gas system from the experimental point of view, the author succeeded in establishing an intermolecular potential, that provides a solid ground for comparison with future ab initio calculations. (Auth.)

  19. Identification of intra- and intermolecular disulfide bridges in the multidrug resistance transporter ABCG2

    DEFF Research Database (Denmark)

    Henriksen, Ulla Birk; Fog, Jacob U; Litman, Thomas

    2005-01-01

    cysteines predicted to be on the extracellular face of ABCG2. Upon mutation of Cys-592 or Cys-608 to alanine (C592A and C608A), ABCG2 migrated as a dimer in SDS-PAGE under non-reducing conditions; however, mutation of Cys-603 to Ala (C603A) caused the transporter to migrate as a single monomeric band....... Despite this change, C603A displayed efficient membrane targeting and preserved transport function. Because the transporter migrated as a dimer in SDS-PAGE, when only Cys-603 was present (C592A-C608A), the data suggest that Cys-603 forms a symmetrical intermolecular disulfide bridge in the ABCG2 homodimer...

  20. Correlations and symmetry of interactions influence collective dynamics of molecular motors

    International Nuclear Information System (INIS)

    Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

    2015-01-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

  1. Kinetics of isotope exchange reactions involving intra- and intermolecular reactions: 1. Rate law for a system with two chemical compounds and three exchangeable atoms

    International Nuclear Information System (INIS)

    Xuelei Chu; Ohmoto, Hiroshi

    1991-01-01

    For an isotopic exchange reaction between two compounds (X and AB) in a homogeneous system, such as a gaseous or aqueous system, where one (AB) of them possesses two exchangeable atoms in non-equivalent positions and where one intramolecular isotope exchange (A ↔ B) and two intermolecular isotope exchange reactions (X ↔ A and X ↔ B) may occur, its rate law no longer obeys a pseudo-first order rate equation described for simple two-component systems by many previous investigators. The change with time of the δ value of each of the three components (X, A, and B) in a closed and homogeneous system is a complicated function of the initial δ values of the three components, the chemical concentrations of the two compounds, and the overall rate constants of the forward and reverse reactions involving the two intermolecular and one intramolecular reactions of isotope exchanges. Also, for some one of the three components, the change of its δ value with time may not be monotonic, and the relationship of 1n (1 - F) with time may be non-linear in a plot of 1n (1 - F) vs. t. In addition, the rate law of the isotope exchange reaction in this system also provides a quantitative method to estimate the overall rate constants for the one-intra-and two intermolecular isotope exchanges and the equilibrium isotopic fractionation factors among the three components

  2. Stability of stationary states of non-local equations with singular interaction potentials

    KAUST Repository

    Fellner, Klemens; Raoul, Gaë l

    2011-01-01

    repulsive interaction potentials we show the stability of stationary states of uniformly bounded solutions under a convexity condition.Finally, we present numerical simulations to illustrate our results. © 2010 Elsevier Ltd.

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

    Directory of Open Access Journals (Sweden)

    Boaz Galdino Oliveira

    2009-08-01

    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 ρ(r, Laplacian Ñ2ρ(r, and ellipticity ε. The examination of the hydrogen bonds has been performed through the measurement of ρ(r, Ñ2ρ(r and ε between (O···H—C and (S···H—C, whereas the secondary interaction between axial hydrogen atoms Hα 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.

  4. Drug-polymer interaction studies of cytarabine loaded chitosan nanoparticles

    International Nuclear Information System (INIS)

    Madni, A.; Kashif, P.M.; Nazir, I.; Rehman, M.

    2017-01-01

    Assessment of possible incompatibilities between drug and excipients is an important parameter of preformulation stage during the pharmaceutical product development of active pharmaceutical ingredient (API). The potential physical and chemical interaction among the components of a delivery system can affect the chemical nature, bioavailability, stability, and subsequently therapeutic efficacy of drugs. In this study, ATR-FTIR spectroscopy was employed to investigate the possible intermolecular interaction of Cytarabine with deacetylated chitosan and tripolyphosphate in the resulting physical blends and crosslinked nanoparticulate system. Two different strategies, physical blending and ionotropic gelation, were adopted to prepare binary or tertiary mixtures and nanoparticulate formulation, respectively. The IR spectra of CB showed characteristic peaks at 3438.27 cm-1 (primary amine), 3264.74 cm-1 (hydroxyl group) and 1654.98 cm-1 (C=O stretch in cyclic ring); CS at 3361.47 cm-1 (N-H stretching), 1646.18 cm-1 (C=O of Amide I), 1582.36 cm-1 (C=O of Amide II), and sTPP at 1135.77 cm-1 (P=O). CS-sTPP chemical interaction was confirmed from the shift in the absorption band of carbonyl groups (amide I, II) to 1634.66 cm-1 and 1541.17 cm-1 in blank chitosan nanoparticles, and 1636.87 cm-1, 1543.33 cm-1 in CSNP1 (2:6:1), and at 1646.15 cm-1 and 1557.04 cm-1 in CSNP2 (1:3:1). The characteristic peaks of CB were also present in chitosan formulation with a slight shift in the amino group at 3429.43 cm-1 and 3423.21 cm-1, in the hydroxyl group at 3274.54 cm-1 and 3270.73 cm-1, CSNP1 and CSNP2, respectively. The findings counseled no significant interaction in IR absorption pattern of cytarabine functional groups after encapsulation in CS-sTPP complex, which projected the potential of chitosan nanoparticulate system to entrap cytarabine. (author)

  5. Use of total cross sections for obtaining the anisotropic interaction potential in atom--diatom system

    International Nuclear Information System (INIS)

    Eccles, J.; Secrest, D.

    1977-01-01

    A study is made of the ''conservation of the total cross section'' and the ''equivalence of the total cross section'' rules for scattering from H 2 . It is shown that these rules are a better approximation than the random phase approximation would indicate. Cross section formulas are given for scattering atoms from m/sub j/ state selected molecules and it is shown that total cross sections for state selected molecules depend on the anisotropic part of the interaction potential, while the spin-averaged total cross section often depends only on the spherically symmetric part of the interaction potential. The total spin-averaged cross section is thus independent of the initial rotation state of the molecule and depends only on the relative collision energy. It is further demonstrated that isotopic substitution, which shifts the center of mass changing the symmetric part of the interaction potential, has too small an effect on the total cross section to be useful as a means of determining the anisotropy of the potential

  6. Molecular dynamics simulations of matrix assisted laser desorption ionization: Matrix-analyte interactions

    International Nuclear Information System (INIS)

    Nangia, Shivangi; Garrison, Barbara J.

    2011-01-01

    There is synergy between matrix assisted laser desorption ionization (MALDI) experiments and molecular dynamics (MD) simulations. To understand analyte ejection from the matrix, MD simulations have been employed. Prior calculations show that the ejected analyte molecules remain solvated by the matrix molecules in the ablated plume. In contrast, the experimental data show free analyte ions. The main idea of this work is that analyte molecule ejection may depend on the microscopic details of analyte interaction with the matrix. Intermolecular matrix-analyte interactions have been studied by focusing on 2,5-dihydroxybenzoic acid (DHB; matrix) and amino acids (AA; analyte) using Chemistry at HARvard Molecular Mechanics (CHARMM) force field. A series of AA molecules have been studied to analyze the DHB-AA interaction. A relative scale of AA molecule affinity towards DHB has been developed.

  7. Theoretical investigation on hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

    Science.gov (United States)

    Anithaa, V S; Vijayakumar, S; Sudha, M; Shankar, R

    2017-11-06

    The interaction of diketo and keto-enol form of thymine and uracil tautomers with acridine (Acr), phenazine (Phen), benzo[c]cinnoline (Ben), 1,10-phenanthroline (1,10-Phe), and 4,7-phenenthroline (4,7-Phe) intercalating drug molecules was studied using density functional theory at B3LYP/6-311++G** and M05-2×/6-311++G** levels of theory. From the interaction energy, it is found that keto-enol form tautomers have stronger interaction with intercalators than diketone form tautomers. On complex formation of thymine and uracil tautomers with benzo[c]cinnoline the drug molecules have high interaction energy values of -20.14 (BenT3) and -20.55 (BenU3) kcal mol -1 , while phenazine has the least interaction energy values of -6.52 (PhenT2) and -6.67 (PhenU2) kcal mol -1 . The closed shell intermolecular type interaction between the molecules with minimum elliptical value of 0.018 and 0.019 a.u at both levels of theory has been found from topological analysis. The benzo[c]cinnoline drug molecule with thymine and uracil tautomers has short range intermolecular N-H…N, C-H…O, and O-H...N hydrogen bonds (H-bonds) resulting in higher stability than other drug molecules. The proper hydrogen bonds N-H..N and O-H..N have the frequency shifted toward the lower side (red shifted) with the elongation in their bond length while the improper hydrogen bond C-H...O has the frequency shifted toward the higher side (blue shifted) of the spectral region with the contraction in their bond length. Further, the charge transfer between proton acceptor and donor along with stability of the bond is studied using natural bond orbital (NBO) analysis. Graphical abstract Hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

  8. Forward detectors around the CMS interaction point at LHC and their physics potential

    CERN Document Server

    Grothe, Monika

    2008-01-01

    Forward physics with CMS at the LHC covers a wide range of physics subjects, including very low-x QCD, underlying event and multiple interactions characteristics, gamma-mediated processes, shower development at the energy scale of primary cosmic ray interactions with the atmosphere, diffraction in the presence of a hard scale and even MSSM Higgs discovery in central exclusive production. We describe the forward detector instrumentation around the CMS interaction point and present selected feasibility studies to illustrate their physics potential.

  9. The Effect of Attractive Interactions and Macromolecular Crowding on Crystallins Association.

    Directory of Open Access Journals (Sweden)

    Jiachen Wei

    Full Text Available In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the clustering of lens proteins, i.e., crystallins, resulting in enhanced light scattering and impaired vision or blindness. To investigate the molecular origins of cataract formation and to design efficient treatments, a better understanding of crystallin association in macromolecular crowded environment is needed. Here we present a theoretical study of simple coarse grained colloidal models to characterize the general features of how the association equilibrium of proteins depends on the magnitude of intermolecular attraction. By comparing the analytic results to the available experimental data on the osmotic pressure in crystallin solutions, we identify the effective parameters regimes applicable to crystallins. Moreover, the combination of two models allows us to predict that the number of binding sites on crystallin is small, i.e. one to three per protein, which is different from previous estimates. We further observe that the crowding factor is sensitive to the size asymmetry between the reactants and crowding agents, the shape of the protein clusters, and to small variations of intermolecular attraction. Our work may provide general guidelines on how to steer the protein interactions in order to control their association.

  10. Perspective: Quantum Hamiltonians for optical interactions

    Science.gov (United States)

    Andrews, David L.; Jones, Garth A.; Salam, A.; Woolley, R. Guy

    2018-01-01

    The multipolar Hamiltonian of quantum electrodynamics is extensively employed in chemical and optical physics to treat rigorously the interaction of electromagnetic fields with matter. It is also widely used to evaluate intermolecular interactions. The multipolar version of the Hamiltonian is commonly obtained by carrying out a unitary transformation of the Coulomb gauge Hamiltonian that goes by the name of Power-Zienau-Woolley (PZW). Not only does the formulation provide excellent agreement with experiment, and versatility in its predictive ability, but also superior physical insight. Recently, the foundations and validity of the PZW Hamiltonian have been questioned, raising a concern over issues of gauge transformation and invariance, and whether observable quantities obtained from unitarily equivalent Hamiltonians are identical. Here, an in-depth analysis of theoretical foundations clarifies the issues and enables misconceptions to be identified. Claims of non-physicality are refuted: the PZW transformation and ensuing Hamiltonian are shown to rest on solid physical principles and secure theoretical ground.

  11. Examining ecological validity in social interaction: problems of visual fidelity, gaze, and social potential.

    Science.gov (United States)

    Reader, Arran T; Holmes, Nicholas P

    2016-01-01

    Social interaction is an essential part of the human experience, and much work has been done to study it. However, several common approaches to examining social interactions in psychological research may inadvertently either unnaturally constrain the observed behaviour by causing it to deviate from naturalistic performance, or introduce unwanted sources of variance. In particular, these sources are the differences between naturalistic and experimental behaviour that occur from changes in visual fidelity (quality of the observed stimuli), gaze (whether it is controlled for in the stimuli), and social potential (potential for the stimuli to provide actual interaction). We expand on these possible sources of extraneous variance and why they may be important. We review the ways in which experimenters have developed novel designs to remove these sources of extraneous variance. New experimental designs using a 'two-person' approach are argued to be one of the most effective ways to develop more ecologically valid measures of social interaction, and we suggest that future work on social interaction should use these designs wherever possible.

  12. Effects of solvent-solute interactions on the stereochemical course in high energy chlorine-38-for chlorine substitution in meso- and rac-1,2-dichloro-1,2-difluoroethane in solution

    International Nuclear Information System (INIS)

    Acciani, T.R.; Su, Y.Y.; Ache, H.J.; Rack, E.P.

    1978-01-01

    The stereochemistry of the chlorine-38-for-chlorine substitution was studied in diastereomeric 1,2-dichloro-1,2-difluoroethanes in solutions. The experimental results are very similar to those previously observed in meso- and d,l-2,4-dichloropentane solutions which by analogy suggest that the stereochemical course of the substitution process is in the present system also predominantly and directly controlled by the properties of the solvent molecules, most likely by the factors which govern the magnitude of intermolecular interaction between reactants and solvents. It appears that strong intermolecular interaction favors substitution via retention of configuration, whereas in solvents having a low dielectric constant the retention/inversion ratio decreases. These results seem further to suggest that if the reaction occurs via the previously postulated caged complex or excited intermediate that the primary attack by the energetic 38 Cl proceeds via both front and backside replacement

  13. Atom-scale molecular interactions in lipid raft mixtures

    DEFF Research Database (Denmark)

    Niemelä, Perttu S; Hyvönen, Marja T; Vattulainen, Ilpo

    2009-01-01

    We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular...... dynamics simulations, complemented by extensive comparison to experimental data. The discussion is divided into four sections. The first part investigates the properties of one-component SM bilayers and compares them to bilayers with phosphatidylcholine (PC), the focus being on a detailed analysis...... examples of this issue. The third part concentrates on the specificity of intermolecular interactions in three-component mixtures of SM, PC and cholesterol (CHOL) under conditions where the concentrations of SM and CHOL are dilute with respect to that of PC. The results show how SM and CHOL favor one...

  14. Hydrogen-Bonding Interactions in Luminescent Quinoline-Triazoles with Dominant 1D Crystals

    Directory of Open Access Journals (Sweden)

    Shi-Qiang Bai

    2017-09-01

    Full Text Available Quinoline-triazoles 2-((4-(diethoxymethyl-1H-1,2,3-triazol-1-ylmethylquinoline (1, 2-((4-(m-tolyl-1H-1,2,3-triazol-1-ylmethylquinoline (2 and 2-((4-(p-tolyl-1H-1,2,3-triazol-1-ylmethylquinoline (3 have been prepared with CuAAC click reactions and used as a model series to probe the relationship between lattice H-bonding interaction and crystal direction of growth. Crystals of 1–3 are 1D tape and prism shapes that correlate with their intermolecular and solvent 1D lattice H-bonding interactions. All compounds were thermally stable up to about 200 C and blue-green emissive in solution.

  15. Drug-drug interactions involving lysosomes: mechanisms and potential clinical implications.

    Science.gov (United States)

    Logan, Randall; Funk, Ryan S; Axcell, Erick; Krise, Jeffrey P

    2012-08-01

    Many commercially available, weakly basic drugs have been shown to be lysosomotropic, meaning they are subject to extensive sequestration in lysosomes through an ion trapping-type mechanism. The extent of lysosomal trapping of a drug is an important therapeutic consideration because it can influence both activity and pharmacokinetic disposition. The administration of certain drugs can alter lysosomes such that their accumulation capacity for co-administered and/or secondarily administered drugs is altered. In this review the authors explore what is known regarding the mechanistic basis for drug-drug interactions involving lysosomes. Specifically, the authors address the influence of drugs on lysosomal pH, volume and lipid processing. Many drugs are known to extensively accumulate in lysosomes and significantly alter their structure and function; however, the therapeutic and toxicological implications of this remain controversial. The authors propose that drug-drug interactions involving lysosomes represent an important potential source of variability in drug activity and pharmacokinetics. Most evaluations of drug-drug interactions involving lysosomes have been performed in cultured cells and isolated tissues. More comprehensive in vivo evaluations are needed to fully explore the impact of this drug-drug interaction pathway on therapeutic outcomes.

  16. The triel bond: a potential force for tuning anion-π interactions

    Science.gov (United States)

    Esrafili, Mehdi D.; Mousavian, Parisasadat

    2018-02-01

    Using ab-initio calculations, the mutual influence between anion-π and B···N or B···C triel bond interactions is investigated in some model complexes. The properties of these complexes are studied by molecular electrostatic potential, noncovalent interaction index, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. According to the results, the formation of B···N or B···C triel bond interactions in the multi-component systems makes a significant shortening of anion-π distance. Such remarkable variation in the anion-π distances has not been reported previously. The strengthening of the anion-π bonding in the multi-component systems depend significantly on the nature of the anion, and it becomes larger in the order Br- > Cl- > F-. The parameters derived from the QTAIM and NBO methodologies are used to study the mechanism of the cooperativity between the anion-π and triel bond interactions in the multi-component complexes.

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

    International Nuclear Information System (INIS)

    Simperler, A.

    1999-03-01

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

  18. Infrared, diode laser spectroscopy of the Ar--N2O complex: Observation of the intermolecular bending mode in combination with the highest frequency intramolecular stretching mode

    International Nuclear Information System (INIS)

    Hu, T.A.; Chappell, E.L.; Sharpe, S.W.

    1993-01-01

    Rotationally resolved vibrational spectra consisting of a-type transitions have been observed for the low-frequency, intermolecular bending mode in combination with the highest frequency, intramolecular stretching mode of Ar--N 2 O. Analysis of the spectral data places the origin of the combination band at 2256.1 cm -1 while the origin of the intramolecular stretching fundamental is at 2223.9 cm -1 . The difference between these two origins is approximately 32.2 cm -1 and agrees well with our calculated frequency of 31.5 cm -1 for the intermolecular bending mode, which was obtained by analysis of the centrifugal distortion constants. In addition, argon--nitrous oxide exhibits an anomalously large inertial defect of 10.96 amu A 2 in the combination state. This indicates a breakdown in the assumption of separation between vibration and rotation. While much of the inertial defect in the ground state can be accounted for by including Coriolis interactions, that occurring in the combination state is only partially accounted for by a similar analysis. Small, but significant changes, are observed in both the radial and angular parameters for Ar--N 2 O when going from the ground to the combination state, indicating large amplitude motion. The combination band is approximately 200 times less intense than the high-frequency, stretching fundamental of Ar--N 2 O. In addition, over 400 new rovibrational transitions are assigned to the previously observed 1 0 1 intramolecular stretching fundamental of the complex, and the subsequent rotational analysis is found to be in close agreement with earlier studies. Data were taken on a newly built, rapid-scan, diode laser spectrometer that incorporates a 12 cmx200 μm pulsed slit-expansion nozzle

  19. A Closer Look at Trends in Boiling Points of Hydrides: Using an Inquiry-Based Approach to Teach Intermolecular Forces of Attraction

    Science.gov (United States)

    Glazier, Samantha; Marano, Nadia; Eisen, Laura

    2010-01-01

    We describe how we use boiling-point trends of group IV-VII hydrides to introduce intermolecular forces in our first-year general chemistry classes. Starting with the idea that molecules in the liquid state are held together by some kind of force that must be overcome for boiling to take place, students use data analysis and critical reasoning to…

  20. Combining density functional and incremental post-Hartree-Fock approaches for van der Waals dominated adsorbate-surface interactions: Ag2/graphene

    International Nuclear Information System (INIS)

    Lara-Castells, María Pilar de; Mitrushchenkov, Alexander O.; Stoll, Hermann

    2015-01-01

    A combined density functional (DFT) and incremental post-Hartree-Fock (post-HF) approach, proven earlier to calculate He-surface potential energy surfaces [de Lara-Castells et al., J. Chem. Phys. 141, 151102 (2014)], is applied to describe the van der Waals dominated Ag 2 /graphene interaction. It extends the dispersionless density functional theory developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] by including periodic boundary conditions while the dispersion is parametrized via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. Starting with the elementary cluster unit of the target surface (benzene), continuing through the realistic cluster model (coronene), and ending with the periodic model of the extended system, modern ab initio methodologies for intermolecular interactions as well as state-of-the-art van der Waals-corrected density functional-based approaches are put together both to assess the accuracy of the composite scheme and to better characterize the Ag 2 /graphene interaction. The present work illustrates how the combination of DFT and post-HF perspectives may be efficient to design simple and reliable ab initio-based schemes in extended systems for surface science applications

  1. Physisorption of three amine terminated molecules (TMBDA, BDA, TFBDA) on the Au(111) Surface: The Role of van der Waals Interaction

    Science.gov (United States)

    Aminpour, Maral; Le, Duy; Rahman, Talat S.

    2012-02-01

    Recently, the electronic properties and alignment of tetramethyl-1,4-benzenediamine (TMBDA), 1,4-benzenediamine (BDA) and tetrafluro-1,4-benzenediamine (TFBDA) molecules were studied experimentally. Discrepancies were found for both the binding energy and the molecule tilt angle with respect to the surface, when results were compared with density functional theory calculations [1]. We have included the effect of vdW interactions both between the molecules and the Au(111) surface and find binding energies which are in very good agreement with experiments. We also find that at low coverages each of these molecules would adsorb almost parallel to the surface. N-Au bond lengths and charge redistribution on adsorption of the molecules are also analyzed. Our calculations are based on DFT using vdW-DF exchange correlation functionals. For BDA (since we are aware of experimental data), we show that for higher coverage, inclusion of intermolecular van der Waals interaction leads to tilting of the molecules with respect to the surface and formation of line structures. Our results demonstrate the central role played by intermolecular interaction in pattern formation on this surface.[4pt] [1] M. Dell'Angela et al, Nano Lett. 2010, 10, 2470; M. Kamenetska et al, J. Phys. Chem. C, 2011, 115, 12625

  2. Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

    Directory of Open Access Journals (Sweden)

    Kei Moritsugu

    2014-10-01

    Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

  3. Cooling of interstellar formaldehyde by collision with helium: an accurate quantum mechanical calculation

    International Nuclear Information System (INIS)

    Garrison, B.J.

    1975-08-01

    In order to test a collisional pumping model as a mechanism for cooling the 6 cm and 2 cm doublets of interstellar formaldehyde, a quantum mechanical scattering calculation is performed. To obtain the intermolecular interaction between H 2 CO( 1 A 1 ) and He( 1 S) two calculations are performed, a Hartree-Fock (HF) potential surface and a configuration interaction (CI) surface. A basis set of better than ''triple zeta plus polarization'' quality is used to compute the HF portion of the potential energy surface. This portion is highly anisotropic and has a slight attraction arising from induction effects at intermolecular separations around 9 a.u. The HF surface is modified through a series of CI calculations. Correlation is found to have little effect in the strongly anisotropic repulsive region of the interaction potential but dominates the well and long-range regions. The maximum well depth is attained for in-plane approaches of He and lies in the range 35-40 0 K for arbitrary theta at center of mass separation of 7.5 a.u. The entire surface is fit to a spherical harmonic expansion to facilitate scattering applications. (auth)

  4. Coupled dynamics of interacting spin-1 bosons in a double-well potential

    Science.gov (United States)

    Carvalho, D. W. S.; Foerster, A.; Gusmão, M. A.

    2018-03-01

    We present a detailed analysis of dynamical processes involving two or three particles in a double-well potential. Motivated by experimental realizations of such a system with optically trapped cold atoms, we focus on spin-1 bosons with special attention on the effects of a spin-dependent interaction in addition to the usual Hubbard-like repulsive one. For a sufficiently weak tunneling amplitude in comparison to the dominant Hubbard coupling, particle motion is strongly correlated, occurring only under fine-tuned relationships between well-depth asymmetry and interactions. We highlight processes involving tunneling of coupled particle pairs and triads, emphasizing the role of the spin-dependent interaction in resonance conditions.

  5. Interactions between Surfactants in Solution and Electrospun Protein Fibers: Effects on Release Behavior and Fiber Properties

    DEFF Research Database (Denmark)

    Boutrup Stephansen, Karen; García-Díaz, María; Jessen, Flemming

    2016-01-01

    , and drug delivery. In the present study, we present a systematic investigation of how surfactants and proteins, as physiologically relevant components, interact with insulin-loaded fish sarcoplasmic protein (FSP) electrospun fibers (FSP-Ins fibers) in solution and thereby affect fiber properties...... such as accessible surface hydrophilicity, physical stability, and release characteristics of an encapsulated drug. Interactions between insulin-loaded protein fibers and five anionic surfactants (sodium taurocholate, sodium taurodeoxycholate, sodium glycocholate, sodium glycodeoxycholate, and sodium dodecyl sulfate......Intermolecular interaction phenomena occurring between endogenous compounds, such as proteins and bile salts, and electrospun compounds are so far unreported, despite the exposure of fibers to such biorelevant compounds when applied for biomedical purposes, e.g., tissue engineering, wound healing...

  6. Potential effect of cationic liposomes on interactions with oral bacterial cells and biofilms.

    Science.gov (United States)

    Sugano, Marika; Morisaki, Hirobumi; Negishi, Yoichi; Endo-Takahashi, Yoko; Kuwata, Hirotaka; Miyazaki, Takashi; Yamamoto, Matsuo

    2016-01-01

    Although oral infectious diseases have been attributed to bacteria, drug treatments remain ineffective because bacteria and their products exist as biofilms. Cationic liposomes have been suggested to electrostatically interact with the negative charge on the bacterial surface, thereby improving the effects of conventional drug therapies. However, the electrostatic interaction between oral bacteria and cationic liposomes has not yet been examined in detail. The aim of the present study was to examine the behavior of cationic liposomes and Streptococcus mutans in planktonic cells and biofilms. Liposomes with or without cationic lipid were prepared using a reverse-phase evaporation method. The zeta potentials of conventional liposomes (without cationic lipid) and cationic liposomes were -13 and 8 mV, respectively, and both had a mean particle size of approximately 180 nm. We first assessed the interaction between liposomes and planktonic bacterial cells with a flow cytometer. We then used a surface plasmon resonance method to examine the binding of liposomes to biofilms. We confirmed the binding behavior of liposomes with biofilms using confocal laser scanning microscopy. The interactions between cationic liposomes and S. mutans cells and biofilms were stronger than those of conventional liposomes. Microscopic observations revealed that many cationic liposomes interacted with the bacterial mass and penetrated the deep layers of biofilms. In this study, we demonstrated that cationic liposomes had higher affinity not only to oral bacterial cells, but also biofilms than conventional liposomes. This electrostatic interaction may be useful as a potential drug delivery system to biofilms.

  7. Estimation of πd-Interactions in Organic Conductors Including Magnetic Anions

    Science.gov (United States)

    Mori, Takehiko; Katsuhara, Mao

    2002-03-01

    Magnetic interactions in organic conductors including magnetic anions, such as λ-(BETS)2FeCl4 and κ-(BETS)2FeX4 [X = Cl and Br], are estimated from intermolecular overlap integrals; the overlaps between anions afford Jdd, and those between anions and donors give Jπ d. From this, the most stable spin alignments are decided, and such quantities as the Néel and Weiss temperatures, as well as the magnitude of spin polarization on the π-molecules are evaluated on the basis of the mean-field theory of πd-systems. The calculation is extended to several other πd-conductors, which are classified depending on the relative magnitudes of the direct dd- and indirect πd-interactions.

  8. Prevalence of potential drug-drug interactions in cancer patients treated with oral anticancer drugs

    NARCIS (Netherlands)

    van Leeuwen, R. W. F.; Brundel, D. H. S.; Neef, C.; van Gelder, T.; Mathijssen, R. H. J.; Burger, D. M.; Jansman, F. G. A.

    2013-01-01

    Background: Potential drug-drug interactions (PDDIs) in patients with cancer are common, but have not previously been quantified for oral anticancer treatment. We assessed the prevalence and seriousness of potential PDDIs among ambulatory cancer patients on oral anticancer treatment. Methods: A

  9. Prevalence of potential drug-drug interactions in cancer patients treated with oral anticancer drugs

    NARCIS (Netherlands)

    R.W.F. van Leeuwen (Roelof); D.H.S. Brundel (D. H S); C. Neef (Cees); T. van Gelder (Teun); A.H.J. Mathijssen (Ron); D.M. Burger (David); F.G.A. Jansman (Frank)

    2013-01-01

    textabstractBackground: Potential drug-drug interactions (PDDIs) in patients with cancer are common, but have not previously been quantified for oral anticancer treatment. We assessed the prevalence and seriousness of potential PDDIs among ambulatory cancer patients on oral anticancer treatment.

  10. Oligophenylenevinylenes in spatially confined nanochannels: Monitoring intermolecular interactions by UV/Vis and Raman spectroscopy

    DEFF Research Database (Denmark)

    Aloshyna, Mariya; Medina, Begona Milian; Poulsen, Lars

    2008-01-01

    -guest interactions are elucidated by UV/Vis and Raman spectroscopy. The impact of the local environment of the chromophore on the optical and photophysical properties is discussed in light of quantum-chemical calculations. In stark contrast to thin films where preferential side-by-side orientation leads to quenching...... of photoluminescence (PL) via non-emissive traps, the ICs are found to be attractive materials for opto-electronic applications: they offer high chromophore concentrations, but at the same time behave as quasi-isolated entities of tightly packed, well-oriented objects with high PL quantum yields and the possibility...

  11. Virus–Bacteria Interactions: Implications and Potential for the Applied and Agricultural Sciences

    Directory of Open Access Journals (Sweden)

    Matthew D. Moore

    2018-02-01

    Full Text Available Eukaryotic virus–bacteria interactions have recently become an emerging topic of study due to multiple significant examples related to human pathogens of clinical interest. However, such omnipresent and likely important interactions for viruses and bacteria relevant to the applied and agricultural sciences have not been reviewed or compiled. The fundamental basis of this review is that these interactions have importance and deserve more investigation, as numerous potential consequences and applications arising from their discovery are relevant to the applied sciences. The purpose of this review is to highlight and summarize eukaryotic virus–bacteria findings in the food/water, horticultural, and animal sciences. In many cases in the agricultural sciences, mechanistic understandings of the effects of virus–bacteria interactions remain unstudied, and many studies solely focus on co-infections of bacterial and viral pathogens. Given recent findings relative to human viral pathogens, further research related to virus–bacteria interactions would likely result in numerous discoveries and beneficial applications.

  12. Virus-Bacteria Interactions: Implications and Potential for the Applied and Agricultural Sciences.

    Science.gov (United States)

    Moore, Matthew D; Jaykus, Lee-Ann

    2018-02-02

    Eukaryotic virus-bacteria interactions have recently become an emerging topic of study due to multiple significant examples related to human pathogens of clinical interest. However, such omnipresent and likely important interactions for viruses and bacteria relevant to the applied and agricultural sciences have not been reviewed or compiled. The fundamental basis of this review is that these interactions have importance and deserve more investigation, as numerous potential consequences and applications arising from their discovery are relevant to the applied sciences. The purpose of this review is to highlight and summarize eukaryotic virus-bacteria findings in the food/water, horticultural, and animal sciences. In many cases in the agricultural sciences, mechanistic understandings of the effects of virus-bacteria interactions remain unstudied, and many studies solely focus on co-infections of bacterial and viral pathogens. Given recent findings relative to human viral pathogens, further research related to virus-bacteria interactions would likely result in numerous discoveries and beneficial applications.

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

    Science.gov (United States)

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

    2008-11-01

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

  14. Synthesis of biological active thiosemicarbazone and characterization of the interaction with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Wangshu; Shi, Lei; Hui, Guangquan [College of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007 (China); Cui, Fengling, E-mail: fenglingcui@hotmail.com [College of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007 (China)

    2013-02-15

    The synthesis of a new biological active reagent, 2-((1,4-dihydroxy)-9,10-anthraquinone) aldehyde thiosemicarbazone (DHAQTS), was designed. The interaction between DHAQTS and HSA was studied by fluorescence spectroscopy in combination with molecular modeling under simulation of physiological conditions. According to the results of fluorescence measurements, the quenching mechanism was suggested to be static. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrophobic interactions are the predominant intermolecular forces stabilizing the complex. The number of binding sites (n) was calculated. Through the site marker competitive experiment, DHAQTS was confirmed to be located in site I of HSA. The binding distance r=2.83 nm between the donor HSA and acceptor DHAQTS was obtained according to Foerster's non-radiative energy transfer theory. The three-dimensional fluorescence spectral results showed the conformation and microenvironment of HSA changed in the presence of DHAQTS. The effects of common ions on the binding of DHAQTS to HSA were also evaluated. The experimental results were in agreement with the results obtained via a molecular docking study. - Highlights: Black-Right-Pointing-Pointer 2-((1,4-dihydroxy)-9,10-anthraquinone)aldehyde thiosemicarbazone (DHAQTS) was synthesized. Black-Right-Pointing-Pointer DHAQTS can quench the fluorescence of human serum albumin (HSA) by static quenching mechanism. Black-Right-Pointing-Pointer Hydrophobic interactions were the predominant intermolecular forces. Black-Right-Pointing-Pointer The competitive experiment was carried out to identify the DHAQTS binding site on HSA. Black-Right-Pointing-Pointer Three-dimensional spectra confirmed DHAQTS caused the conformational change of HSA.

  15. Calculation of parameters of the interaction potential between excited alkali atoms and mercury atoms: The Cs*, Pr*-Hg interaction

    International Nuclear Information System (INIS)

    Glushkov, A.V.

    1994-01-01

    Based on the method of effective potential involving the new polarization interaction potential calculated from polarization diagrams of the perturbation theory in the Thomas-Fermi approximation, the main parameters of the interatomic potentials (equilibrium distances, potential well depth) are evaluated for a system consisting of an alkali atom in the ground and excited states and of a mercury atom. The results of calculations of quasi-molecular terms for the A-Hg system, where A = Na, Cs, Fr, are reported, some of which are obtained for the first time. A comparison is made with available experimental and theoretical data. 29 refs., 2 figs., 1 tab

  16. Combining density functional and incremental post-Hartree-Fock approaches for van der Waals dominated adsorbate-surface interactions: Ag{sub 2}/graphene

    Energy Technology Data Exchange (ETDEWEB)

    Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es [Instituto de Física Fundamental (C.S.I.C.), Serrano 123, E-28006 Madrid (Spain); Mitrushchenkov, Alexander O. [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Stoll, Hermann [Institut für Theoretische Chemie, Universität Stuttgart, D-70550 Stuttgart (Germany)

    2015-09-14

    A combined density functional (DFT) and incremental post-Hartree-Fock (post-HF) approach, proven earlier to calculate He-surface potential energy surfaces [de Lara-Castells et al., J. Chem. Phys. 141, 151102 (2014)], is applied to describe the van der Waals dominated Ag{sub 2}/graphene interaction. It extends the dispersionless density functional theory developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] by including periodic boundary conditions while the dispersion is parametrized via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. Starting with the elementary cluster unit of the target surface (benzene), continuing through the realistic cluster model (coronene), and ending with the periodic model of the extended system, modern ab initio methodologies for intermolecular interactions as well as state-of-the-art van der Waals-corrected density functional-based approaches are put together both to assess the accuracy of the composite scheme and to better characterize the Ag{sub 2}/graphene interaction. The present work illustrates how the combination of DFT and post-HF perspectives may be efficient to design simple and reliable ab initio-based schemes in extended systems for surface science applications.

  17. Drivers potentially influencing host-bat fly interactions in anthropogenic neotropical landscapes at different spatial scales.

    Science.gov (United States)

    Hernández-Martínez, Jacqueline; Morales-Malacara, Juan B; Alvarez-Añorve, Mariana Yolotl; Amador-Hernández, Sergio; Oyama, Ken; Avila-Cabadilla, Luis Daniel

    2018-05-21

    The anthropogenic modification of natural landscapes, and the consequent changes in the environmental conditions and resources availability at multiple spatial scales can affect complex species interactions involving key-stone species such as bat-parasite interactions. In this study, we aimed to identify the drivers potentially influencing host-bat fly interactions at different spatial scales (at the host, vegetation stand and landscape level), in a tropical anthropogenic landscape. For this purpose, we mist-netted phyllostomid and moormopid bats and collected the bat flies (streblids) parasitizing them in 10 sites representing secondary and old growth forest. In general, the variation in fly communities largely mirrored the variation in bat communities as a result of the high level of specialization characterizing host-bat fly interaction networks. Nevertheless, we observed that: (1) bats roosting dynamics can shape bat-streblid interactions, modulating parasite prevalence and the intensity of infestation; (2) a degraded matrix could favor crowding and consequently the exchange of ectoparasites among bat species, lessening the level of specialization of the interaction networks and promoting novel interactions; and (3) bat-fly interaction can also be shaped by the dilution effect, as a decrease in bat diversity could be associated with a potential increase in the dissemination and prevalence of streblids.

  18. Theoretical study of hydrogen bond interactions of fluvastatin with ι-carrageenan and λ-carrageenan.

    Science.gov (United States)

    Papadopoulos, Anastasios G; Sigalas, Michael P

    2011-07-01

    The binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug's release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three low energy conformers of fluvastatin have been calculated. The vibrational spectroscopic properties calculated for the most stable conformer were in satisfactory agreement with the experimental data. A series of hydrogen bonded complexes of the most stable conformer of fluvastatin anion with low molecular weight models of the polymers have been fully optimized. In almost all, intermolecular H-bonds are formed between the sulfate groups of ι- or λ-carrageenan and fluvastatin's hydroxyls, resulting in a red shift of the fluvastatin's O - H stretching vibrations. Cooperative intramolecular H-bonds within fluvastatin or ι-, λ-carrageenan are also present. The BSSE and ZPE corrected interaction energies were estimated in the range 281-318 kJ mol⁻¹ for ι-carrageenan - fluvastatin and 145-200 kJ mol⁻¹ for λ-carrageenan - fluvastatin complexes. The electron density (ρ (bcp)) and Laplacian (∇²ρ (bcp)) properties at critical points of the intermolecular hydrogen bonds, estimated by AIM (atoms in molecules) calculations, have a low and positive character (∇²ρ(bcp) > 0), consistent with the electrostatic character of the hydrogen bonds. The structural and energetic data observed, as well as the extent of the red shift of the fluvastatin's O - H stretching vibrations upon complex formation and the properties of electron density show a stronger binding of fluvastatin to ι- than to λ-carrageenan.

  19. Comparison of the effect of soft-core potentials and Coulombic potentials on bremsstrahlung during laser matter interaction

    Science.gov (United States)

    Pandit, Rishi R.; Becker, Valerie R.; Barrington, Kasey; Thurston, Jeremy; Ramunno, Lora; Ackad, Edward

    2018-04-01

    An intense, short laser pulse incident on rare-gas clusters can produce nano-plasmas containing energetic electrons. As these electrons undergo scattering, from both phonons and ions, they emit bremsstrahlung radiation. Here, we compare a theory of bremsstrahlung emission appropriate for the interaction of intense lasers with matter using soft-core potentials and Coulombic potentials. A new scaling for the radiation cross-section and the radiated power via bremsstrahlung is derived for a soft-core potential (which depends on the potential depth) and compared with the Coulomb potential. Calculations using the new scaling are performed for electrons in vacuum ultraviolet, infrared and mid-infrared laser pulses. The radiation cross-section and the radiation power via bremsstrahlung are found to increase rapidly with increases in the potential depth of up to around 200 eV and then become mostly saturated for larger depths while remaining constant for the Coulomb potential. In both cases, the radiation cross-section and the radiation power of bremsstrahlung decrease with increases in the laser wavelength. The ratio of the scattering amplitude for the soft-core potential and that for the Coulombic potential decreases exponentially with an increase in momentum transfer. The bremsstrahlung emission by electrons in plasmas may provide a broadband light source for diagnostics.

  20. Single-particle potential of the Λ hyperon in nuclear matter with chiral effective field theory NLO interactions including effects of Y N N three-baryon interactions

    Science.gov (United States)

    Kohno, M.

    2018-03-01

    Adopting hyperon-nucleon and hyperon-nucleon-nucleon interactions parametrized in chiral effective field theory, single-particle potentials of the Λ and Σ hyperons are evaluated in symmetric nuclear matter and in pure neutron matter within the framework of lowest-order Bruckner theory. The chiral NLO interaction bears strong Λ N -Σ N coupling. Although the Λ potential is repulsive if the coupling is switched off, the Λ N -Σ N correlation brings about the attraction consistent with empirical data. The Σ potential is repulsive, which is also consistent with empirical information. The interesting result is that the Λ potential becomes shallower beyond normal density. This provides the possibility of solving the hyperon puzzle without introducing ad hoc assumptions. The effects of the Λ N N -Λ N N and Λ N N -Σ N N three-baryon forces are considered. These three-baryon forces are first reduced to normal-ordered effective two-baryon interactions in nuclear matter and then incorporated in the G -matrix equation. The repulsion from the Λ N N -Λ N N interaction is of the order of 5 MeV at normal density and becomes larger with increasing density. The effects of the Λ N N -Σ N N coupling compensate the repulsion at normal density. The net effect of the three-baryon interactions on the Λ single-particle potential is repulsive at higher densities.

  1. Interaction potentials for multiquark states from instantons and other background gauge field configurations

    International Nuclear Information System (INIS)

    Warner, R.C.; Joshi, G.C.

    1979-01-01

    A simple rule is presented for calculating the contributions to the interaction potentials between constituent particles for a family of multiquark states, due to the presence of a semi-classical gauge field configuration which exists in a single SU(2) subgroup of colour SU(3). In multiquark states beyond the baryon many-body potential terms are found. The static (Wilson loop) limit is sufficient to elucidate the dependence of the potential on the colour structure of the multiquark state

  2. Self-assembly of Hydrazide-based Heterodimers Driven by Hydrogen Bonding and Donor-Acceptor Interaction

    Institute of Scientific and Technical Information of China (English)

    FENG,Dai-Jun; WANG,Peng; LI,Xiao-Qiang; LI,Zhan-Ting

    2006-01-01

    A new series of hydrogen bonding-driven heterodimers have been self-assembled in chloroform from hydrazide-based monomers. Additional intermolecular donor-acceptor interaction between the electron-rich bis(p-phenylene)-34-crown-10 unit and the electron-deficient naphthalene diimide unit has been utilized to increase the stability of the dimmers, and pronounced cooperativity of the two discrete non-covalent forces to stabilize the dimer has been revealed by the quantitative 1H (2D) NMR and UV-Vis experiments.

  3. Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

    International Nuclear Information System (INIS)

    Zhou Shiqi

    2005-01-01

    A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.

  4. Metal complexes of alkyl-aryl dithiocarbamates: Structural studies, anticancer potentials and applications as precursors for semiconductor nanocrystals

    Science.gov (United States)

    Andrew, Fartisincha P.; Ajibade, Peter A.

    2018-03-01

    Dithiocarbamates are versatile ligands able to stabilize wide range of metal ions in their various oxidation states with the partial double bond character of Csbnd N and Csbnd S of thioureide moiety. Variation of the substituents attached to the nitrogen atom of dithiocarbamate moiety generates various intermolecular interactions, which lead to different structural arrangement in the solid state. The presence of bulky substituents on the N atom obviates the supramolecular aggregation via secondary Msbnd S interactions whereas smaller substituents encourage such aggregation that results in their wide properties and applications. Over the past decades, the synthesis and structural studies of metal complexes of dithiocarbamates have received considerable attention as potential anticancer agents with various degree of DNA binding affinity and cytotoxicity and as single molecule precursors for the preparation of semiconductor nanocrystals. In this paper, we review the synthesis, structural studies, anticancer potency and the use of alkyl-phenyl dithiocarbamate complexes as precursors for the preparation of semiconductor nanocrystals. The properties of these compounds and activities are ascribed to be due to either the dithiocarbamate moieties, the nature or type of the substituents around the dithiocarbamate backbone and the central metal ions or combination of these factors.

  5. Adverse event potentially due to an interaction between ibrutinib and verapamil: a case report.

    Science.gov (United States)

    Lambert Kuhn, E; Levêque, D; Lioure, B; Gourieux, B; Bilbault, P

    2016-02-01

    Ibrutinib is a recently approved oral anticancer agent with pharmacokinetics that is very sensitive to metabolic inhibition. We report a serious side effect of ibrutinib potentially attributable to interaction with the moderate CYP3A4 inhibitor verapamil. A patient with mantle cell lymphoma was admitted to our emergency department with severe diarrhoea. During a prescription review, the clinical pharmacist identified a potential drug interaction between ibrutinib and verapamil present in a branded combination product also containing trandolapril. Ibrutinib was discontinued for 5 days, and verapamil was stopped. Lercanidipine 10 mg daily was prescribed as an alternative antihypertensive drug. The patient was discharged after 3 days with symptomatic treatment for his diarrhoea. Three months later, the patient maintained control with ibrutinib and olmesartan, but without verapamil. This is the first description of a serious side effect of ibrutinib likely due to an interaction with the CYP3A4 inhibitor verapamil. Prescriptions of ibrutinib must be carefully checked to identify possible interactions with CYP3A4 inhibitors and patients monitored accordingly. © 2016 John Wiley & Sons Ltd.

  6. Comparison of Leptospira interrogans and Leptospira biflexa genomes: analysis of potential leptospiral-host interactions.

    Science.gov (United States)

    Mehrotra, Prachi; Ramakrishnan, Gayatri; Dhandapani, Gunasekaran; Srinivasan, Narayanaswamy; Madanan, Madathiparambil G

    2017-05-02

    Leptospirosis, a potentially life-threatening disease, remains the most widespread zoonosis caused by pathogenic species of Leptospira. The pathogenic spirochaete, Leptospira interrogans, is characterized by its ability to permeate human host tissues rapidly and colonize multiple organs in the host. In spite of the efforts taken to comprehend the pathophysiology of the pathogen and the heterogeneity posed by L. interrogans, the current knowledge on the mechanism of pathogenesis is modest. In an attempt to contribute towards the same, we demonstrate the use of an established structure-based protocol coupled with information on subcellular localization of proteins and their tissue-specificity, in recognizing a set of 49 biologically feasible interactions potentially mediated by proteins of L. interrogans in humans. We have also presented means to adjudge the physicochemical viability of the predicted host-pathogen interactions, for selected cases, in terms of interaction energies and geometric shape complementarity of the interacting proteins. Comparative analyses of proteins of L. interrogans and the saprophytic spirochaete, Leptospira biflexa, and their predicted involvement in interactions with human hosts, aided in underpinning the functional relevance of leptospiral-host protein-protein interactions specific to L. interrogans as well as those specific to L. biflexa. Our study presents characteristics of the pathogenic L. interrogans that are predicted to facilitate its ability to persist in human hosts.

  7. Improving the first hyperpolarizability of anthracene through interaction with HX molecules (Xdbnd F, Cl, Br): A theoretical study

    Science.gov (United States)

    Abdolmaleki, Ahmad; Dadsetani, Mehrdad; Zabardasti, Abedin

    2018-05-01

    The variations in nonlinear optical activity (NLO) of anthracene (C14H10) was investigated via intermolecular interactions between C14H10 and HX molecules (Xdbnd F, Cl and Br) using B3LYP-D3 method at 6-311++G(d,p) basis set. The stabilization of those complexes was investigated via vibrational analysis, quantum theory of atoms in molecules, molecular electrostatic potential, natural bond orbitals and symmetry-adapted perturbation theory (SAPT) analysis. Furthermore, the optical spectra and the first hyperpolarizabilities of C14H10⋯HX complexes were computed. The adsorption of hydrogen halide through C14H10⋯HX complex formation, didn't change much the linear optical activities of C14H10 molecule, but the magnitude of the first hyperpolarizability of the C14H10⋯HX complexes to be as much as that of urea.

  8. Assessment of the Performance of MP2 and MP2 Variants for the Treatment of Noncovalent Interactions

    Czech Academy of Sciences Publication Activity Database

    Riley, Kevin Eugene; Platts, J. A.; Řezáč, Jan; Hobza, Pavel; Hill, J. G.

    2012-01-01

    Roč. 116, č. 16 (2012), s. 4159-4169 ISSN 1089-5639 R&D Projects: GA ČR GBP208/12/G016 Grant - others:European Social Fund(XE) CZ1.05/2.1.00/03/0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : plesset perturbation-theory * density-functional-theory * intermolecular interaction energies * molecular-orbital methods * auxiliary basis-sets * ab-initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.771, year: 2012

  9. Tunable interactions between paramagnetic colloidal particles driven in a modulated ratchet potential.

    Science.gov (United States)

    Straube, Arthur V; Tierno, Pietro

    2014-06-14

    We study experimentally and theoretically the interactions between paramagnetic particles dispersed in water and driven above the surface of a stripe patterned magnetic garnet film. An external rotating magnetic field modulates the stray field of the garnet film and generates a translating potential landscape which induces directed particle motion. By varying the ellipticity of the rotating field, we tune the inter-particle interactions from net repulsive to net attractive. For attractive interactions, we show that pairs of particles can approach each other and form stable doublets which afterwards travel along the modulated landscape at a constant mean speed. We measure the strength of the attractive force between the moving particles and propose an analytically tractable model that explains the observations and is in quantitative agreement with experiment.

  10. Frequency of potential interactions between drugs in medical prescriptions in a city in southern Brazil

    Directory of Open Access Journals (Sweden)

    Genici Weyh Bleich

    Full Text Available CONTEXT AND OBJECTIVE: Drug interactions form part of current clinical practice and they affect between 3 and 5% of polypharmacy patients. The aim of this study was to identify the frequency of potential drug-drug interactions in prescriptions for adult and elderly patients. TYPE OF STUDY AND SETTING: Cross-sectional pharmacoepidemiological survey in the Parque Verde housing project, municipality of Cascavel, Paraná, Brazil, between December 2006 and February 2007. METHODS: Stratified cluster sampling, proportional to the total number of homes in the housing project, was used. The sample consisted of 95 homes and 96 male or female patients aged 19 or over, with medical prescriptions for at least two pharmaceutical drugs. Interactions were identified using DrugDigest, Medscape and Micromedex softwares. RESULTS: Most of the patients were female (69.8%, married (59.4% and in the age group of 60 years or over (56.3%, with an income less than or equal to three minimum monthly salaries (81.3% and less than eight years of schooling (69.8%; 90.6% of the patients were living with another person. The total number of pharmaceutical drugs was 406 (average of 4.2 medications per patient. The drugs most prescribed were antihypertensives (47.5%. The frequency of drug interactions was 66.6%. Among the 154 potential drug interactions, 4.6% were classified as major, 65.6% as moderate and 20.1% as minor. CONCLUSION: The high frequency of drug prescriptions with a potential for differentiated interactions indicates a situation that has so far been little explored, albeit a reality in household surveys.

  11. The Prevalence of Potential Drug Interactions Among Critically Ill Elderly Patients in the Intensive Care Unit (ICU

    Directory of Open Access Journals (Sweden)

    Hossein Rafiei

    2012-01-01

    Full Text Available Objectives: The aim of the research was to determine prevalence of potential drug interactions among elderly patients in the Shahid Bahonar ICU in Kerman. Methods & Materials: In this cross sectional study, data about all elderly patients who were admitted in the intensive care unit from 1/4/2009 to 1/4/2010 were retrieved from medical records and evaluated with regard to the number and type of drug interactions, the number of drugs administered, age, sex, length of stay in the ICU, and the number of doctors prescribing medications of medications administered. The extent and number of drug interactions were investigated based on the reference textbook Drug Interaction Facts and in order to analyze the data collected, using SPSS 18 and according to study goals, a descriptive test, Pierson's correlation test, an independent T-test and a one-way ANOVA were used. Results: In total, 77 types of drugs and 394 drugs were prescribed with a mean of 5.6(SD=1.5 drugs per patient. A total of 108 potential drug interactions were found related to drugs prescribed during the first twenty-four hours. In terms of the type of drug interactions, delayed, moderate and possible types comprised the highest proportion of drug interactions. The four major interactions were between cimetidine and methadone, furosemide and amikacine, phenytoin and dopamine, and heparin and aspirin. The results of Pierson's correlation test were inicative of a positive correlation between the number of potential drug interactions and that of the drugs prescribed (r=0.563, P<0.05. Results of a one-way ANOVA showed that the mean number of potential drug interaction were significantly higher in those who died than in other patients (P<0.05. Conclusion: Elderly patients who are admitted to the intensive care unit are at a high risk of developing drug interactions and better care must be taken by medical team members.

  12. Potential herb-drug interactions found in a community pharmacy patients

    OpenAIRE

    C. Batista; C. Pinho; M. Castel-Branco; M. Caramona; I. Figueiredo

    2015-01-01

    Phytotherapy has always played a leading role in therapeutics. However, a strong knowledge of the risk-benefit relationship of herbal products by patients and health professionals is necessary. The goals of this study were to characterize the consumption pattern of medicinal plants in patients in a community pharmacy, identify potential herb-drug interactions, and establish a list of recommendations for health professionals and/or patients in order to prevent/minimize negative outcomes arisin...

  13. A molecular dynamics calculation of solid phase of malonic acid

    Indian Academy of Sciences (India)

    Recent studies suggest that hydrogen bonds, in particular, hydrogen bond chains play an important role in determining the properties of a substance.We report an investigation into the triclinic phase of crystalline malonic acid. One of two intermolecular interaction potentials proposed here is seen to predict the lattice ...

  14. Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

    Science.gov (United States)

    Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

    2015-08-14

    We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

  15. Reconstruction of the Tip-Surface Interaction Potential by Analysis of the Brownian Motion of an Atomic Force Microscope Tip

    NARCIS (Netherlands)

    Willemsen, O.H.; Kuipers, L.; van der Werf, Kees; de Grooth, B.G.; Greve, Jan

    2000-01-01

    The thermal movement of an atomic force microscope (AFM) tip is used to reconstruct the tip-surface interaction potential. If a tip is brought into the vicinity of a surface, its movement is governed by the sum of the harmonic cantilever potential and the tip-surface interaction potential. By

  16. A trans-Complementing Recombination Trap Demonstrates a Low Propensity of Flaviviruses for Intermolecular Recombination▿

    Science.gov (United States)

    Taucher, Christian; Berger, Angelika; Mandl, Christian W.

    2010-01-01

    Intermolecular recombination between the genomes of closely related RNA viruses can result in the emergence of novel strains with altered pathogenic potential and antigenicity. Although recombination between flavivirus genomes has never been demonstrated experimentally, the potential risk of generating undesirable recombinants has nevertheless been a matter of concern and controversy with respect to the development of live flavivirus vaccines. As an experimental system for investigating the ability of flavivirus genomes to recombine, we developed a “recombination trap,” which was designed to allow the products of rare recombination events to be selected and amplified. To do this, we established reciprocal packaging systems consisting of pairs of self-replicating subgenomic RNAs (replicons) derived from tick-borne encephalitis virus (TBEV), West Nile virus (WNV), and Japanese encephalitis virus (JEV) that could complement each other in trans and thus be propagated together in cell culture over multiple passages. Any infectious viruses with intact, full-length genomes that were generated by recombination of the two replicons would be selected and enriched by end point dilution passage, as was demonstrated in a spiking experiment in which a small amount of wild-type virus was mixed with the packaged replicons. Using the recombination trap and the JEV system, we detected two aberrant recombination events, both of which yielded unnatural genomes containing duplications. Infectious clones of both of these genomes yielded viruses with impaired growth properties. Despite the fact that the replicon pairs shared approximately 600 nucleotides of identical sequence where a precise homologous crossover event would have yielded a wild-type genome, this was not observed in any of these systems, and the TBEV and WNV systems did not yield any viable recombinant genomes at all. Our results show that intergenomic recombination can occur in the structural region of flaviviruses

  17. Sense-antisense (complementary) peptide interactions and the proteomic code; potential opportunities in biology and pharmaceutical science.

    Science.gov (United States)

    Miller, Andrew D

    2015-02-01

    A sense peptide can be defined as a peptide whose sequence is coded by the nucleotide sequence (read 5' → 3') of the sense (positive) strand of DNA. Conversely, an antisense (complementary) peptide is coded by the corresponding nucleotide sequence (read 5' → 3') of the antisense (negative) strand of DNA. Research has been accumulating steadily to suggest that sense peptides are capable of specific interactions with their corresponding antisense peptides. Unfortunately, although more and more examples of specific sense-antisense peptide interactions are emerging, the very idea of such interactions does not conform to standard biology dogma and so there remains a sizeable challenge to lift this concept from being perceived as a peripheral phenomenon if not worse, into becoming part of the scientific mainstream. Specific interactions have now been exploited for the inhibition of number of widely different protein-protein and protein-receptor interactions in vitro and in vivo. Further, antisense peptides have also been used to induce the production of antibodies targeted to specific receptors or else the production of anti-idiotypic antibodies targeted against auto-antibodies. Such illustrations of utility would seem to suggest that observed sense-antisense peptide interactions are not just the consequence of a sequence of coincidental 'lucky-hits'. Indeed, at the very least, one might conclude that sense-antisense peptide interactions represent a potentially new and different source of leads for drug discovery. But could there be more to come from studies in this area? Studies on the potential mechanism of sense-antisense peptide interactions suggest that interactions may be driven by amino acid residue interactions specified from the genetic code. If so, such specified amino acid residue interactions could form the basis for an even wider amino acid residue interaction code (proteomic code) that links gene sequences to actual protein structure and function, even

  18. Effect of donor orientation on ultrafast intermolecular electron transfer in coumarin-amine systems

    International Nuclear Information System (INIS)

    Singh, P. K.; Nath, S.; Bhasikuttan, A. C.; Kumbhakar, M.; Mohanty, J.; Sarkar, S. K.; Mukherjee, T.; Pal, H.

    2008-01-01

    Effect of donor amine orientation on nondiffusive ultrafast intermolecular electron transfer (ET) reactions in coumarin-amine systems has been investigated using femtosecond fluorescence upconversion measurements. Intermolecular ET from different aromatic and aliphatic amines used as donor solvents to the excited coumarin-151 (C151) acceptor occurs with ultrafast rates such that the shortest fluorescence lifetime component (τ 1 ) is the measure of the fastest ET rate (τ 1 =τ ET fast =(k ET fast ) -1 ), assigned to the C151-amine contact pairs in which amine donors are properly oriented with respect to C151 to maximize the acceptor-donor electronic coupling (V el ). It is interestingly observed that as the amine solvents are diluted by suitable diluents (either keeping solvent dielectric constant similar or with increasing dielectric constant), the τ 1 remains almost in the similar range as long as the amine dilution does not cross a certain critical limit, which in terms of the amine mole fraction (x A ) is found to be ∼0.4 for aromatic amines and ∼0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the τ 1 values are seen to increase very sharply. The large difference in the critical x A values involving aromatic and aliphatic amine donors has been rationalized in terms of the largely different orientational restrictions for the ET reactions as imposed by the aliphatic (n-type) and aromatic (π-type) nature of the amine donors [A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008)]. Since the highest occupied molecular orbital (HOMO) of the n-type aliphatic amines is mostly centralized at the amino nitrogen, only some specific orientations of these amines with respect to the close-contact acceptor dye [also of π-character; A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008) and E. W. Castner et al., J. Phys. Chem. A 104, 2869 (2000)] can give suitable V el and thus ultrafast ET reaction. In contrary, the

  19. Mean Field Limits for Interacting Diffusions in a Two-Scale Potential

    Science.gov (United States)

    Gomes, S. N.; Pavliotis, G. A.

    2018-06-01

    In this paper, we study the combined mean field and homogenization limits for a system of weakly interacting diffusions moving in a two-scale, locally periodic confining potential, of the form considered in Duncan et al. (Brownian motion in an N-scale periodic potential, arXiv:1605.05854, 2016b). We show that, although the mean field and homogenization limits commute for finite times, they do not, in general, commute in the long time limit. In particular, the bifurcation diagrams for the stationary states can be different depending on the order with which we take the two limits. Furthermore, we construct the bifurcation diagram for the stationary McKean-Vlasov equation in a two-scale potential, before passing to the homogenization limit, and we analyze the effect of the multiple local minima in the confining potential on the number and the stability of stationary solutions.

  20. Inelastic multiple scattering of interacting bosons in weak random potentials

    International Nuclear Information System (INIS)

    Geiger, Tobias

    2013-01-01

    Within the present thesis we develop a diagrammatic scattering theory for interacting bosons in a three-dimensional, weakly disordered potential. Based on a microscopic N-body scattering theory, we identify the relevant diagrams including elastic and inelastic collision processes that are sufficient to describe quantum transport in the regime of weak disorder. By taking advantage of the statistical properties of the weak disorder potential, we demonstrate how the N-body dynamics can be reduced to a nonlinear integral equation of Boltzmann type for the single-particle diffusive flux. A presently available alternative description - based on the Gross-Pitaevskii equation - only includes elastic collisions. In contrast, we show that far from equilibrium the presence of inelastic collisions - even for weak interaction strength - must be accounted for and can induce the full thermalization of the single-particle current. In addition, we also determine the coherent corrections to the incoherent transport, leading to the effect of coherent backscattering. For the first time, we are able to analyze the influence of inelastic collisions on the coherent backscattering signal, which lead to an enhancement of the backscattered cone in a narrow spectral window, even for increasing non-linearity. With a short recollection of the presently available experimental techniques we furthermore show how an immediate implementation of our suggested setup with confined Bose-Einstein condensates can be accomplished. Thereby, the emergence of collective and/or thermodynamic behavior from fundamental, microscopic constituents can also be assessed experimentally. In a second part of this thesis, we present first results for light scattering off strongly interacting Rydberg atoms trapped in a one-dimensional, chain-like configuration. In order to monitor the time-dependence of this interacting many-body system, we devise a weak measurement scenario for which we derive a master equation for the