WorldWideScience

Sample records for binding energy

  1. Binding Energy and Enzymatic Catalysis.

    Science.gov (United States)

    Hansen, David E.; Raines, Ronald T.

    1990-01-01

    Discussed is the fundamental role that the favorable free energy of binding of the rate-determining transition state plays in catalysis. The principle that all of the catalytic factors discussed are realized by the use of this binding energy is reviewed. (CW)

  2. Predicting binding free energies in solution

    CERN Document Server

    Jensen, Jan H

    2015-01-01

    Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While the paper is primarily a synthesis of previously published work there are two new results: the adaptation of Legendre transformed free energies to electronic structure theory and a use of water clusters that maximizes error cancellation in binding free energies computed using explicit solvent molecules. While I focus on binding free energies in aqueous solution the approach also a...

  3. Binding energy of two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Singh, Jai; Birkedal, Dan; Vadim, Lyssenko;

    1996-01-01

    Using a model structure for a two-dimensional (2D) biexciton confined in a quantum well, it is shown that the form of the Hamiltonian of the 2D biexciton reduces into that of an exciton. The binding energies and Bohr radii of a 2D biexciton in its various internal energy states are derived...... analytically using the fractional dimension approach. The ratio of the binding energy of a 2D biexciton to that of a 2D exciton is found to be 0.228, which agrees very well with the recent experimental value. The results of our approach are compared with those of earlier theories....

  4. Binding energies of hypernuclei and hypernuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R. [Argonne National Lab., IL (United States)]|[Univ. of Illinois, Chicago, IL (United States). Dept. of Physics; Murali, S.; Usmani, Q.N. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

    1996-05-01

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

  5. The binding energy and bonding in dialane.

    Science.gov (United States)

    Goebbert, Daniel J; Hernandez, Heriberto; Francisco, Joseph S; Wenthold, Paul G

    2005-08-24

    The binding energy of dialane, Al2H6, has been measured using mass spectrometric techniques to be 33 +/- 5 kcal/mol. This represents the first measurement of the thermochemical properties of dialane, which has only recently been observed in low-temperature matricies. High-level quantum mechanical calculations give a binding energy in agreement with the measured value. Experimental and quantum mechanical calculations show that dialane is chemically similar to diborane, B2H6, even though the bonding for these two systems shows significant differences.

  6. Binding Energy and Equilibrium of Compact Objects

    Directory of Open Access Journals (Sweden)

    Germano M.

    2014-04-01

    Full Text Available The theoretical analysis of the existence of a limit mass for compact astronomic ob- jects requires the solution of the Einstein’s equations of g eneral relativity together with an appropriate equation of state. Analytical solutions exi st in some special cases like the spherically symmetric static object without energy sou rces that is here considered. Solutions, i.e. the spacetime metrics, can have a singular m athematical form (the so called Schwarzschild metric due to Hilbert or a nonsingula r form (original work of Schwarzschild. The former predicts a limit mass and, conse quently, the existence of black holes above this limit. Here it is shown that, the origi nal Schwarzschild met- ric permits compact objects, without mass limit, having rea sonable values for central density and pressure. The lack of a limit mass is also demonst rated analytically just imposing reasonable conditions on the energy-matter densi ty, of positivity and decreas- ing with radius. Finally the ratio between proper mass and to tal mass tends to 2 for high values of mass so that the binding energy reaches the lim it m (total mass seen by a distant observer. As it is known the negative binding energ y reduces the gravitational mass of the object; the limit of m for the binding energy provides a mechanism for stable equilibrium of any amount of mass to contrast the gravitatio nal collapse.

  7. Divacancy binding energy, formation energy and surface energy of BCC transition metals using MEAM potentials

    Science.gov (United States)

    Uniyal, Shweta; Chand, Manesh; Joshi, Subodh; Semalty, P. D.

    2016-05-01

    The modified embedded atom method (MEAM) potential parameters have been employed to calculate the unrelaxed divacancy formation energy, binding energy and surface energies for low index planes in bcc transition metals. The calculated results of divacancy binding energy and vacancy formation energy compare well with experimental and other available calculated results.

  8. Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

    Science.gov (United States)

    Mentes, Ahmet; Deng, Nan-Jie; Vijayan, R S K; Xia, Junchao; Gallicchio, Emilio; Levy, Ronald M

    2016-05-10

    Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom and accelerate sampling of intramolecular degrees of freedom relevant to protein-ligand binding. The method is tested on a standard benchmark (T4 Lysozyme/L99A/p-xylene complex) and on a library of HIV-1 integrase complexes derived from the SAMPL4 blind challenge. We applied the torsional flattening strategy to 26 of the 53 known binders to the HIV Integrase LEDGF site found to have a binding energy landscape funneled toward the crystal structure. We show that our approach samples the conformational space more efficiently than the original method without flattening when starting from a poorly docked pose with incorrect ligand dihedral angle conformations. In these unfavorable cases convergence to a binding pose within 2-3 Å from the crystallographic pose is obtained within a few nanoseconds of the Hamiltonian replica exchange simulation. We found that torsional flattening is insufficient in cases where trapping is due to factors other than torsional energy, such as the formation of incorrect intramolecular hydrogen bonds and stacking. Work is in progress to generalize the approach to handle these cases and thereby make it more widely applicable.

  9. Yukawa-dissociation and the deuteron binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Jacobsen, T.

    1997-05-01

    It is shown that energy must be conserved by the dissociation of an elementary particle. The energy deficit by a dissociation behaves as a basic concept. The binding energy of the deuteron is reproduced. 4 refs.

  10. Extrapolations of nuclear binding energies from new linear mass relations

    DEFF Research Database (Denmark)

    Hove, D.; Jensen, A. S.; Riisager, K.

    2013-01-01

    We present a method to extrapolate nuclear binding energies from known values for neighboring nuclei. We select four specific mass relations constructed to eliminate smooth variation of the binding energy as function nucleon numbers. The fast odd-even variations are avoided by comparing nuclei...

  11. Influence of binding energies of electrons on nuclear mass predictions

    Science.gov (United States)

    Tang, Jing; Niu, Zhong-Ming; Guo, Jian-You

    2016-07-01

    Nuclear mass contains a wealth of nuclear structure information, and has been widely employed to extract the nuclear effective interactions. The known nuclear mass is usually extracted from the experimental atomic mass by subtracting the masses of electrons and adding the binding energy of electrons in the atom. However, the binding energies of electrons are sometimes neglected in extracting the known nuclear masses. The influence of binding energies of electrons on nuclear mass predictions are carefully investigated in this work. If the binding energies of electrons are directly subtracted from the theoretical mass predictions, the rms deviations of nuclear mass predictions with respect to the known data are increased by about 200 keV for nuclei with Z, N ⩾ 8. Furthermore, by using the Coulomb energies between protons to absorb the binding energies of electrons, their influence on the rms deviations is significantly reduced to only about 10 keV for nuclei with Z, N ⩾ 8. However, the binding energies of electrons are still important for the heavy nuclei, about 150 keV for nuclei around Z = 100 and up to about 500 keV for nuclei around Z = 120. Therefore, it is necessary to consider the binding energies of electrons to reliably predict the masses of heavy nuclei at an accuracy of hundreds of keV. Supported by National Natural Science Foundation of China (11205004)

  12. Atomic Mass and Nuclear Binding Energy for F-35 (Fluorine)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope F-35 (Fluorine, atomic number Z = 9, mass number A = 35).

  13. Binding energy of donors in symmetric triangular quantum wells

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ji-ye; LIANG Xi-xia

    2005-01-01

    Hydrogen-like donor impurity states in symmetric triangular quantum wells are investigated by using a variational method.Both the effects of the variable effective mass of electrons and the spatially dependent dielectric constant are considered in the calculation.The numerical results show that the binding energy depends on not only the effective mass and dielectric constant but also the spatial distribution of electron probability density.The binding energies of donor states get the maximums at the well-center.The results are also compared with those obtained in parabolic and square wells.It is seen that the triangular well support the highest binding energies for donor states.

  14. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  15. Predicting accurate absolute binding energies in aqueous solution

    DEFF Research Database (Denmark)

    Jensen, Jan Halborg

    2015-01-01

    Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic. In this paper I summarize some of the many factors that could easily contribute 1-3 kcal......-represented by continuum models. While I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational or reaction free energy differences or activation free energies in any solvent....

  16. Relativistic calculation of the triton binding energy and its implications

    CERN Document Server

    Stadler, A; Stadler, Alfred; Gross, Franz

    1996-01-01

    First results for the triton binding energy obtained from the relativistic spectator or Gross equation are reported. The Dirac structure of the nucleons is taken into account. Numerical results are presented for a family of realistic OBE models with off-shell scalar couplings. It is shown that these off-shell couplings improve both the fits to the two-body data and the predictions for the binding energy.

  17. Atomic Mass and Nuclear Binding Energy for Ra-226 (Radium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Ra-226 (Radium, atomic number Z = 88, mass number A = 226).

  18. Binding energies and modelling of nuclei in semiclassical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Perez-Garcia, M. Angeles [Departamento de Fisica Fundamental and Instituto Universitario de Fisica Fundamental y Matematicas, IUFFyM, Universidad de Salamanca, Plaza de la Merced s/n 37008 Salamanca (Spain)], E-mail: mperezga@usal.es; Tsushima, K. [Departamento de Fisica Fundamental and Instituto Universitario de Fisica Fundamental y Matematicas, IUFFyM, Universidad de Salamanca, Plaza de la Merced s/n 37008 Salamanca (Spain)], E-mail: tsushima@usal.es; Valcarce, A. [Departamento de Fisica Fundamental and Instituto Universitario de Fisica Fundamental y Matematicas, IUFFyM, Universidad de Salamanca, Plaza de la Merced s/n 37008 Salamanca (Spain)], E-mail: valcarce@usal.es

    2008-03-06

    We study the binding energies of spin-isospin saturated nuclei with nucleon number 8{<=}A{<=}100 in semiclassical Monte Carlo many-body simulations. The model Hamiltonian consists of (i) nucleon kinetic energy, (ii) a nucleon-nucleon interaction potential, and (iii) an effective Pauli potential which depends on density. The basic ingredients of the nucleon-nucleon potential are a short-range repulsion, and a medium-range attraction. Our results demonstrate that one can always expect to obtain the empirical binding energies for a set of nuclei by introducing a proper density dependent Pauli potential in terms of a single variable, the nucleon number, A. The present work shows that in the suggested procedure there is a delicate counterbalance of kinetic and potential energetic contributions allowing a good reproduction of the experimental nuclear binding energies. This type of calculations may be of interest in further reproduction of other properties of nuclei such as radii and also exotic nuclei.

  19. Accurate nuclear radii and binding energies from a chiral interaction

    CERN Document Server

    Ekstrom, A; Wendt, K A; Hagen, G; Papenbrock, T; Carlsson, B D; Forssen, C; Hjorth-Jensen, M; Navratil, P; Nazarewicz, W

    2015-01-01

    The accurate reproduction of nuclear radii and binding energies is a long-standing challenge in nuclear theory. To address this problem two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective 3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

  20. Predicting accurate absolute binding energies in aqueous solution

    DEFF Research Database (Denmark)

    Jensen, Jan Halborg

    2015-01-01

    Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic. In this paper I summarize some of the many factors that could easily contribute 1-3 kcal...... mol(-1) errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well......-represented by continuum models. While I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational or reaction free energy differences or activation free energies in any solvent....

  1. Binding Energy of Excitons in a Quantum Ring

    Institute of Scientific and Technical Information of China (English)

    XIE Wen-Fang

    2008-01-01

    The binding energy of excitons confined to a quantum ring under the influence of perpendicular homogeneous magnetic field is calculated as a function of the ring radius. Calculations are made by using the method of exact diagonalization within the effective-mass approximation. The feature of binding energy of the ground state as a function of the ring radius for several values of the magnetic field has been revealed. The interesting feature of our study is that, in a quantum ring, the geometric structure of excitons may reveal transition.

  2. Binding energy and fine structure of the He- ion

    Institute of Scientific and Technical Information of China (English)

    ZHUO; Lin; ZHU; Jing-jing; GOU; Bing-cong

    2007-01-01

    The variational method using a multiconfiguration wavefunction is carried out on the core-excited state 1s2s2p 4P0 for helium negative ion, including mass polarization and relativistic corrections. Binding energy and fine structure are reported. The results are compared with other theoretical and experimental date in the literature.

  3. Core level photoemission of rotaxanes : A summary on binding energies

    NARCIS (Netherlands)

    Mendoza, S. M.; Berna, J.; Perez, E. M.; Kay, E. R.; Mateo-Alonso, A.; De Nadai, C.; Zhang, S.; Baggerman, J.; Wiering, P. G.; Leigh, D. A.; Prato, M.; Brouwer, A.M.; Rudolf, P.; Nadaï, C. De

    2008-01-01

    Several rotaxanes were studied by XPS in the form of thin films or monolayers on gold substrates. Here we report a database of photoemission spectra of the C 1s, N 1s and F 1s core levels. Binding energy ranges are summarized, classifying the core levels according to the chemical groups that form pa

  4. Core level photoemission of rotaxanes: A summary on binding energies

    Energy Technology Data Exchange (ETDEWEB)

    Mendoza, S.M. [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands); Berna, J.; Perez, E.M.; Kay, E.R. [School of Chemistry, University of Edinburgh, King' s Buildings, West Mains Road, Edinburgh EH9 3JJ (United Kingdom); Mateo-Alonso, A. [Dipartimento di Scienze Farmaceutiche, Universita di Trieste, Piazzale Europa 1, 34127 Trieste (Italy); De Nadai, C. [Laboratoire Interdisciplinaire de Spectroscopie Electronique, Facultes Universitaires Notre Dame de la Paix, 61 Rue de Bruxelles, B-5000 Namur (Belgium); Zhang, S. [School of Chemistry, University of Edinburgh, King' s Buildings, West Mains Road, Edinburgh EH9 3JJ (United Kingdom); Baggerman, J.; Wiering, P.G. [Van' t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, NL-1018 WS Amsterdam (Netherlands); Leigh, D.A. [School of Chemistry, University of Edinburgh, King' s Buildings, West Mains Road, Edinburgh EH9 3JJ (United Kingdom); Prato, M. [Dipartimento di Scienze Farmaceutiche, Universita di Trieste, Piazzale Europa 1, 34127 Trieste (Italy); Brouwer, A.M. [Van' t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, NL-1018 WS Amsterdam (Netherlands); Rudolf, P. [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands)], E-mail: P.Rudolf@rug.nl

    2008-09-15

    Several rotaxanes were studied by XPS in the form of thin films or monolayers on gold substrates. Here we report a database of photoemission spectra of the C 1s, N 1s and F 1s core levels. Binding energy ranges are summarized, classifying the core levels according to the chemical groups that form part of the rotaxanes.

  5. Alternate Energy Sources for Thermalplastic Binding Agent Consolidation

    Energy Technology Data Exchange (ETDEWEB)

    Frame, B.J.

    1999-01-01

    A study was conducted to investigate microwave and electron beam technologies as alternate energy sources to consolidate fiber coated with a thermoplastic binding agent into preforms for composite molding applications. Bench experiments showed that both microwave and electron beam energy can produce heat sufficient to melt and consolidate a thermoplastic binding agent applied to fiberglass mat, and several two- and three-dimensional fiberglass preforms were produced with each method. In both cases, it is postulated that the heating was accomplished by the effective interaction of the microwave or electron beam energy with the combination of the mat preform and the tooling used to shape the preform. Both methods contrast with conventional thermal energy applied via infrared heaters or from a heated tool in which the heat to melt the thermoplastic binding agent must diffuse over time from the outer surface of the preform toward its center under a thermal gradient. For these reasons, the microwave and electron beam energy techniques have the potential to rapidly consolidate thick fiber preforms more efficiently than the thermal process. With further development, both technologies have the potential to make preform production more cost effective by decreasing cycle time in the preform tool, reducing energy costs, and by enabling the use of less expensive tooling materials. Descriptions of the microwave and electron beam consolidation experiments and a summary of the results are presented in this report.

  6. Core level binding energies of functionalized and defective graphene.

    Science.gov (United States)

    Susi, Toma; Kaukonen, Markus; Havu, Paula; Ljungberg, Mathias P; Ayala, Paola; Kauppinen, Esko I

    2014-01-01

    X-ray photoelectron spectroscopy (XPS) is a widely used tool for studying the chemical composition of materials and it is a standard technique in surface science and technology. XPS is particularly useful for characterizing nanostructures such as carbon nanomaterials due to their reduced dimensionality. In order to assign the measured binding energies to specific bonding environments, reference energy values need to be known. Experimental measurements of the core level signals of the elements present in novel materials such as graphene have often been compared to values measured for molecules, or calculated for finite clusters. Here we have calculated core level binding energies for variously functionalized or defected graphene by delta Kohn-Sham total energy differences in the real-space grid-based projector-augmented wave density functional theory code (GPAW). To accurately model extended systems, we applied periodic boundary conditions in large unit cells to avoid computational artifacts. In select cases, we compared the results to all-electron calculations using an ab initio molecular simulations (FHI-aims) code. We calculated the carbon and oxygen 1s core level binding energies for oxygen and hydrogen functionalities such as graphane-like hydrogenation, and epoxide, hydroxide and carboxylic functional groups. In all cases, we considered binding energy contributions arising from carbon atoms up to the third nearest neighbor from the functional group, and plotted C 1s line shapes by using experimentally realistic broadenings. Furthermore, we simulated the simplest atomic defects, namely single and double vacancies and the Stone-Thrower-Wales defect. Finally, we studied modifications of a reactive single vacancy with O and H functionalities, and compared the calculated values to data found in the literature.

  7. Exciton and Biexciton Binding Energies in Rectangular Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    LIU Yong-Hui; KONG Xiao-Jun

    2005-01-01

    @@ In the effective mass approximation, using the variational technology and a method of expanding the wavefunctions of exciton in terms of the eigenfunctions of the noninteracting electron-hole system, we calculate the exciton and biexciton ground state binding energies for rectangular quantum dots (QDs). In the calculation, a three-dimensional Fourier expansion of Coulomb potential is used to remove the numerical difficulty with the 1/r singularity, and it considerably reduces the computational effort. Our results agree fairly well with the previous results. It is found that the binding energies are highly correlated to the size of QDs. The quantum confinement effect of spherical QDs about biexciton is obviously larger than that of rectangular QDs when the well width is narrower than 2.0aB.

  8. Impurity binding energy for -doped quantum well structures

    Indian Academy of Sciences (India)

    V Tulupenko; C A Duque; R Demediuk; O Fomina; V Akimov; V Belykh; T Dmitrichenko; V Poroshin

    2014-10-01

    The binding energy of an impurity delta layer situated either in the centre or at the edge of a quantum well (QW) is theoretically considered for the example of -type Si0.8Ge0.2/Si/Si0.8Ge0.2 QW doped with phosphorus. Calculations are made for the case of not so big impurity concentrations, when impurity bands are not yet formed and it is still possible to treat impurity as isolated ones. It is shown on the base of self-consistent solution of Schrödinger, Poisson and electro-neutrality equations that impurity binding energy is dependent on the degree of impurity ionization and the most noticeably for the case of edge-doped QWs.

  9. Bose polaron problem: Effect of mass imbalance on binding energy

    Science.gov (United States)

    Ardila, L. A. Peña; Giorgini, S.

    2016-12-01

    By means of quantum Monte Carlo methods we calculate the binding energy of an impurity immersed in a Bose-Einstein condensate at T =0 . The focus is on the attractive branch of the Bose polaron and on the role played by the mass imbalance between the impurity and the surrounding particles. For an impurity resonantly coupled to the bath, we investigate the dependence of the binding energy on the mass ratio and on the interaction strength within the medium. In particular, we determine the equation of state in the case of a static (infinite mass) impurity, where three-body correlations are irrelevant and the result is expected to be a universal function of the gas parameter. For the mass ratio corresponding to 40K impurities in a gas of 87Rb atoms, we provide an explicit comparison with the experimental findings of a recent study carried out at JILA.

  10. Nuclear binding energy using semi empirical mass formula

    Science.gov (United States)

    Ankita, Suthar, B.

    2016-05-01

    In the present communication, semi empirical mass formula using the liquid drop model has been presented. Nuclear binding energies are calculated using semi empirical mass formula with various constants given by different researchers. We also compare these calculated values with experimental data and comparative study for finding suitable constants is added using the error plot. The study is extended to find the more suitable constant to reduce the error.

  11. Improvement in a phenomenological formula for ground state binding energies

    CERN Document Server

    Gangopadhyay, G

    2016-01-01

    The phenomenological formula for ground state binding energy derived earlier (International Journal of Modern Physics E {\\bf 20} (2011) 179) has been modified. The parameters have been obtained by fitting the latest available tabulation of experimental values. The major modifications include a new term for pairing and introduction of a new neutron magic number at $N=160$. The new formula reduced the root mean square deviation to 363 keV, a substantial improvement over the previous version of the formula.

  12. Binding energy of the $X(3872)$ at unphysical pion masses

    CERN Document Server

    Baru, V; Filin, A A; Gegelia, J; Nefediev, A V

    2015-01-01

    Chiral extrapolation of the $X(3872)$ binding energy is investigated using the modified Weinberg formulation of chiral effective field theory for the $D \\bar{D}^*$ scattering. Given its explicit renormalisability, this approach is particularly useful to explore the interplay of the long- and short-range $D \\bar{D}^*$ forces in the $X(3872)$ from studying the light-quark (pion) mass dependence of its binding energy. In particular, the parameter-free leading-order calculation shows that the $X$-pole disappears for unphysical large pion masses. On the other hand, without contradicting the naive dimensional analysis, the higher-order pion-mass-dependent contact interaction can change the slope of the binding energy at the physical point yielding the opposite scenario of a stronger bound $X$ at pion masses larger than its physical value. An important role of the pion dynamics and of the 3-body $D\\bar{D}\\pi$ effects for chiral extrapolations of the $X$-pole is emphasised. The results of the present study should be ...

  13. Precise determination of neutron binding energy of 64Cu

    Science.gov (United States)

    Telezhnikov, S. A.; Granja, C.; Honzatko, J.; Pospisil, S.; Tomandl, I.

    2016-05-01

    The neutron binding energy in 64Cu has been accurately measured in thermal neutron capture. A composite target of natural Cu and NaCl was used on a high flux neutron beam using a large measuring time. The γ-ray spectrum emitted in the ( n, γ) reaction was measured with a HPGe detector in large statistics (up to 106 events per channel). Intrinsic limitations of HPGe detectors, which restrict the accuracy of energy calibration, were determined. The value B n of 64Cu was determined as 7915.867(24) keV.

  14. Phosphate binding energy and catalysis by small and large molecules.

    Science.gov (United States)

    Morrow, Janet R; Amyes, Tina L; Richard, John P

    2008-04-01

    Catalysis is an important process in chemistry and enzymology. The rate acceleration for any catalyzed reaction is the difference between the activation barriers for the uncatalyzed (Delta G(HO)(#)) and catalyzed (Delta G(Me)(#)) reactions, which corresponds to the binding energy (Delta G(S)(#) = Delta G(Me)(#)-Delta G(HO)(#)) for transfer of the reaction transition state from solution to the catalyst. This transition state binding energy is a fundamental descriptor of catalyzed reactions, and its evaluation is necessary for an understanding of any and all catalytic processes. We have evaluated the transition state binding energies obtained from interactions between low molecular weight metal ion complexes or high molecular weight protein catalysts and the phosphate group of bound substrate. Work on catalysis by small molecules is exemplified by studies on the mechanism of action of Zn2(1)(H2O). A binding energy of Delta G(S)(#) = -9.6 kcal/mol was determined for Zn2(1)(H2O)-catalyzed cleavage of the RNA analogue HpPNP. The pH-rate profile for this cleavage reaction showed that there is optimal catalytic activity at high pH, where the catalyst is in the basic form [Zn2(1)(HO-)]. However, it was also shown that the active form of the catalyst is Zn2(1)(H2O) and that this recognizes the C2-oxygen-ionized substrate in the cleavage reaction. The active catalyst Zn2(1)(H2O) shows a high affinity for oxyphosphorane transition state dianions and a stable methyl phosphate transition state analogue, compared with the affinity for phosphate monoanion substrates. The transition state binding energies, Delta G(S)(#), for cleavage of HpPNP catalyzed by a variety of Zn2+ and Eu3+ metal ion complexes reflect the increase in the catalytic activity with increasing total positive charge at the catalyst. These values of Delta G(S)(#) are affected by interactions between the metal ion and its ligands, but these effects are small in comparison with Delta G(S)(#) observed for catalysis

  15. Binding Energy Calculations for Novel Ternary Ionic Lattices

    Science.gov (United States)

    Rodríguez-Mijangos, Ricardo; Vazquez-Polo, Gustavo

    2002-03-01

    Theoretical calculations for the binding energy between metalic ions and negative ions on a novel ternary ionic lattice is carried out for several solid solutions prepared with different concentrations and characterized recently (1). The ternary lattices that reach a good miscibility are: KCl(x)KBr(y)RbCl(z) in three different concentrations: (x=y=z=0.33), (x=0.5, y=0.25, z=0.25) and (x=0.33, y=0.07, z=0.60). The binding energy for these novel structures is calculated from the lattice constants obtained by X ray diffractometry analysis performed on the samples and the Vegard law (2). For the repulsive force exponent m, an average of the m values was considered. The energy values obtained by the Born´expression are compared with corresponding energy values from the lattice with more complex expressions, such as the Born Mayer, Born-Van der Walls. There is a good aggreement between all these calculations. (1)R. R. Mijangos, A. Cordero-Borboa, E. Alvarez, M. Cervantes, Physics Letters A 282 (2001) 195-200. (2) G. Vazquez-Polo, R. R. Mijangos et al. Revista Mexicana de Fisica, 47, Diciembre 2001. In Press.

  16. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors.

    Science.gov (United States)

    Peón, Antonio; Coderch, Claire; Gago, Federico; González-Bello, Concepción

    2013-05-01

    Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.

  17. Binding energies of CO2 with some ionic liquids

    Science.gov (United States)

    Eucker, William; Bendler, John

    2007-03-01

    Room temperature ionic liquids (RTILs), a novel class of materials with negligible vapor pressures and potentiality as benign solvents, may be an ideal chemical for carbon dioxide (CO2) gas sequestration. Ab initio computational modeling was used to investigate the molecular interactions of simple RTIL anions hexafluorophosphate (PF6^-) and tetrafluoroborate (BF4^-) with CO2. Electronic potential energy surface (PES) scans of a comprehensive sampling of 1:1 anion-CO2 orientations were computed using Spartan '02 with Dunning's correlation consistent basis sets. Qualitatively, the PES scans yielded deeper, more numerous and radially closer active sites surrounding BF4^- anion as compared with the PF6^- anion. Quantitatively, the binding energies of 17.87 kJ/mol and 25.24 kJ/mol were extracted from the identified global energy minima for the PF6^- and BF4^- systems, respectively. The smaller BF4^- anion was concluded to bind more strongly to the CO2. However, literature-reported experimental Henry's law constants for CO2 dissolved in imidizolium based RTILs show greater gas solvation in the PF6^- system. The discrepancy between the energetics calculation results and the experimental solvation data will be discussed.

  18. DFT calculation of core-electron binding energies

    Energy Technology Data Exchange (ETDEWEB)

    Takahata, Yuji; Chong, Delano P. E-mail: chong@chem.ubc.ca

    2003-11-01

    A total of 59 core-electron binding energies (CEBEs) were studied with the Amsterdam Density Functional Program (ADF) program and compared with the observed values. The results indicate that a polarized triple-zeta basis set of Slater-type orbitals is adequate for routine assessment of the performance of each method of computation. With such a basis set, seven density functionals were tested. In addition, the performance of 21 energy density functionals were computed from the density calculated with the statistical average of orbital potentials (SAOP). Among all the choices tested, the best density functional for core-electron binding energies of C to F turns out to be the combination of Perdew-Wang (1986) functional for exchange and the Perdew-Wang (1991) functional for correlation, confirming earlier studies based on contracted Gaussian-type orbitals. For this best functional, five Slater-type orbital basis sets were examined, ranging from polarized double-zeta quality to the largest set available in the ADF package. For the best functional with the best basis set, the average absolute deviation (AAD) of the calculated value from experiment is only 0.16 eV.

  19. Biexciton binding energy in ZnSe quantum wells and quantum wires

    DEFF Research Database (Denmark)

    Wagner, Hans-Peter; Langbein, Wolfgang; Hvam, Jørn Märcher

    2002-01-01

    The biexciton binding energy E-XX is investigated in ZnSe/ZnMgSe quantum wells and quantum wires as a function of the lateral confinement by transient four-wave mixing. In the quantum wells one observes for decreasing well width a significant increase in the relative binding energy, saturating...... the experimentally observed dependence of the biexciton binding energies....

  20. Many-body approximations for atomic binding energies

    CERN Document Server

    Schuster, Micah D; Staker, Joshua T

    2011-01-01

    We benchmark three approximations for the many-body problem -- the Hartree-Fock, projected Hartree-Fock, and random phase approximations -- against full numerical configuration-interaction calculations of the electronic structure of atoms, from Li through to Ne. Each method uses exactly the same input, i.e., the same single-particle basis and Coulomb matrix elements, so any differences are strictly due to the approximation itself. Although it consistently overestimates the ground state binding energy, the random phase approximation has the smallest overall errors; furthermore, we suggest it may be useful as a method for efficient optimization of single-particle basis functions.

  1. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    Science.gov (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  2. An Accurate Redetermination of the $^{118}Sn$ Binding Energy

    CERN Document Server

    Borzakov, S B; Faikow-Stanczyk, H; Grigoriev, Yu V; Panteleev, T; Pospísil, S; Smotritsky, L M; Telezhnikov, S A

    2001-01-01

    The energy of well-known strong {gamma}-line from {{^198}Au}, the "gold standard", has been modified in the light of new adjustments in the fundamental constants and the value of 411.80176(12) keV was determined which is 0.29 eV lower than the latest 1999 value. An energy calibration procedure for determining the neutron binding energy, {B_n}, from complicated {(n , gamma)}-spectra has been developed. A mathematically simple minimization function consisting only of terms having as parameters the coefficients of the energy calibration curve (polynomial) is used. A priori information about the relationships among the energies of different peaks on the spectrum is taking into account by a Monte Carlo simulation. The procedure was used in obtaining of {B_n} for {{^118}Sn} and {{^64}Cu}. The {gamma}-ray spectrum from thermal neutron radiative capture by {{^117}Sn} has been measured on the IBR-2 pulsed reactor. {gamma}-rays were detected by a 72 cm^3 HPGe-detector. {B_n} for {{^64}Cu} was obtained from two {gamma}-...

  3. La- binding energies by analysis of its photodetachment spectra

    Science.gov (United States)

    Pan, Lin; Beck, Donald R.

    2016-06-01

    This study reinterprets an earlier experimental photoelectron kinetic energy spectrum of the negative ion of lanthanum [A. M. Covington, D. Calabrese, J. S. Thompson, and T. J. Kvale, J. Phys. B 31, L855 (1998), 10.1088/0953-4075/31/20/002] by carrying out relativistic configuration interaction (RCI) photodetachment calculations. The results confirm the earlier RCI calculation for the electron affinity of lanthanum (0.545 eV) [S. M. O'Malley and D. R. Beck, Phys. Rev. A 79, 012511 (2009), 10.1103/PhysRevA.79.012511] and revise it to a slightly larger value of 0.550 eV, thus modifying the experimental interpretation of 0.47 ±0.02 eV. The calculation also yields the binding energies of the other thirteen bound states of La-. Good agreement has been found when these energies are compared to the results of a recent experimental study on La- [C. W. Walter, N. D. Gibson, D. J. Matyas, C. T. Crocker, K. A. Dungan, B. R. Matola, and J. Rohlén, Phys. Rev. Lett. 113, 063001 (2014), 10.1103/PhysRevLett.113.063001]. Finally, our analysis confirms the transition energy for the potential laser cooling transition of 3F2e→3D1o in La-.

  4. Double binding energy differences: Mean-field or pairing effect?

    Science.gov (United States)

    Qi, Chong

    2012-10-01

    In this Letter we present a systematic analysis on the average interaction between the last protons and neutrons in atomic nuclei, which can be extracted from the double differences of nuclear binding energies. The empirical average proton-neutron interaction Vpn thus derived from experimental data can be described in a very simple form as the interplay of the nuclear mean field and the pairing interaction. It is found that the smooth behavior as well as the local fluctuations of the Vpn in even-even nuclei with N ≠ Z are dominated by the contribution from the proton-neutron monopole interactions. A strong additional contribution from the isoscalar monopole interaction and isovector proton-neutron pairing interaction is seen in the Vpn for even-even N = Z nuclei and for the adjacent odd-A nuclei with one neutron or proton being subtracted.

  5. Binding Energies of a Positively Charged Exciton in a Quantum Disc

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The binding energies of the lowest singlet and triplet states of positively charged excitons confined to a quantum disc are studied using exact diagonalization techniques. We investigate the dependence of the binding energies on the confinement strength and on the effective electron-to-hole mass ratio. The results we have obtained show that the binding energies are closely correlated to the strength of the confinement potential and the effective electron-to-hole mass ratio.

  6. Quantum-Confinement Effects on Binding Energies and Optical Properties of Excitons in Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    潘晖

    2004-01-01

    Quantum-confinement effects on the binding energy and the linear optical susceptibility of excitons in quantum dots are studied. It is found that the binding energy and the linear optical susceptibility are sensitive to the barrier height and the dot size. For an infinite barrier, the binding energy of excitons decreases monotonically with the increasing dot radius, and the absorption intensity has almost the same amplitude with the increasing photon energy. For a finite barrier, the binding energy has a maximum value with the increasing dot radius, and the absorption intensity damps rapidly with the increasing photon energy. The effective mass ratio is also found to have an influence on the binding energy. The results could be confirmed by future experiments on excitons in quantum dots.

  7. Determination of energies and sites of binding of PFOA and PFOS to human serum albumin.

    Science.gov (United States)

    Salvalaglio, Matteo; Muscionico, Isabella; Cavallotti, Carlo

    2010-11-25

    Structure and energies of the binding sites of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) to human serum albumin (HSA) were determined through molecular modeling. The calculations consisted of a compound approach based on docking, followed by molecular dynamics simulations and by the estimation of the free binding energies adopting WHAM-umbrella sampling and semiempirical methodologies. The binding sites so determined are common either to known HSA fatty acids sites or to other HSA sites known to bind to pharmaceutical compounds such as warfarin, thyroxine, indole, and benzodiazepin. Among the PFOA binding sites, five have interaction energies in excess of -6 kcal/mol, which become nine for PFOS. The calculated binding free energy of PFOA to the Trp 214 binding site is the highest among the PFOA complexes, -8.0 kcal/mol, in good agreement with literature experimental data. The PFOS binding site with the highest energy, -8.8 kcal/mol, is located near the Trp 214 binding site, thus partially affecting its activity. The maximum number of ligands that can be bound to HSA is 9 for PFOA and 11 for PFOS. The calculated data were adopted to predict the level of complexation of HSA as a function of the concentration of PFOA and PFOS found in human blood for different levels of exposition. The analysis of the factors contributing to the complex binding energy permitted to outline a set of guidelines for the rational design of alternative fluorinated surfactants with a lower bioaccumulation potential.

  8. Determining binding energies of valence-band electrons in insulators and semiconductors via lanthanide spectroscopy

    NARCIS (Netherlands)

    Dorenbos, P.

    2013-01-01

    Models and methods to determine the absolute binding energy of 4f-shell electrons in lanthanide dopants will be combined with data on the energy of electron transfer from the valence band to a lanthanide dopant. This work will show that it provides a powerful tool to determine the absolute binding e

  9. Effect of the isovector coupling channel on the macroscopic part of the nuclear binding energy

    Indian Academy of Sciences (India)

    S Haddad

    2013-05-01

    The effect of isovector coupling channel on the macroscopic part of the nuclear binding energy is studied using the relativistic density-dependent Thomas–Fermi approach. The dependency of this effect on the number of neutrons and protons is also studied. The isovector coupling channel leads to increased nuclear binding energy, and this effect increases with the increasing neutron number in the nucleus.

  10. The Effect of Chemical Composition and Structure on XPS Binding Energies in Zeolites

    NARCIS (Netherlands)

    Weckhuysen, B.M.; Gijzeman, O.L.J.; Mens, A.J.M.; Lenthe, J.H. van; Mortier, W.J.

    2003-01-01

    The effect of zeolite composition and structure on XPS core level binding energies has been studied for a large class of zeolites (FAU, MFI, MOR, LTA) differing in their counterions (Na, K, Rb, Ca, Mg, Ba) and Si:Al ratio (1 to 160). Whereas absolute binding energies cannot be determined to any reas

  11. CLiBE: a database of computed ligand binding energy for ligand-receptor complexes.

    Science.gov (United States)

    Chen, X; Ji, Z L; Zhi, D G; Chen, Y Z

    2002-11-01

    Consideration of binding competitiveness of a drug candidate against natural ligands and other drugs that bind to the same receptor site may facilitate the rational development of a candidate into a potent drug. A strategy that can be applied to computer-aided drug design is to evaluate ligand-receptor interaction energy or other scoring functions of a designed drug with that of the relevant ligands known to bind to the same binding site. As a tool to facilitate such a strategy, a database of ligand-receptor interaction energy is developed from known ligand-receptor 3D structural entries in the Protein Databank (PDB). The Energy is computed based on a molecular mechanics force field that has been used in the prediction of therapeutic and toxicity targets of drugs. This database also contains information about ligand function and other properties and it can be accessed at http://xin.cz3.nus.edu.sg/group/CLiBE.asp. The computed energy components may facilitate the probing of the mode of action and other profiles of binding. A number of computed energies of some PDB ligand-receptor complexes in this database are studied and compared to experimental binding affinity. A certain degree of correlation between the computed energy and experimental binding affinity is found, which suggests that the computed energy may be useful in facilitating a qualitative analysis of drug binding competitiveness.

  12. Free energy of binding of a small molecule to an amorphous polymer in a solvent.

    Science.gov (United States)

    Chunsrivirot, Surasak; Trout, Bernhardt L

    2011-06-01

    Crystallization is a commonly used purification process in industrial practice. It usually begins with heterogeneous nucleation on a foreign surface. The complicated mechanism of heterogeneous nucleation is not well understood, but we hypothesize that a possible correlation between binding affinity to a surface and nucleation enhancement might exist. Amorphous polymers have been used in controlling crystallization. However, to our knowledge, no attempt has been made to calculate the free energy of binding of a small molecule to an amorphous polymer in a solvent, and to characterize the binding sites/conformations of this system at a molecular level. We developed a two-step approach, first using Adsorption Locator to identify probable binding sites and molecular dynamics to screen for the best binding sites and then using the Blue-Moon Ensemble method to compute the free energy of binding. A system of ethylene glycol, polyvinyl alcohol (PVA), and heavy water (D(2)O) was used for validation, since experimental data exists on a related system. Looking at four independently constructed surfaces, we found that ethylene glycol binds to an indentation on the surface or in a hole beneath the surface. We focused on the indentation binding sites because they are easily accessible and do not have large free energy barriers. The closest system for which experimental data on binding energetics exists is ethylene glycol on PVA in aqueous solutions/gels, and the magnitudes of the free energy of binding to the three best indentation binding sites are close to the experimental value, 0.4-3.7 kcal/mol higher. Our approach offers a way to compute the free energy of binding and characterize the binding sites/conformations, and is general enough to apply to other small molecule/amorphous polymer/solvent systems.

  13. A Prediction Method of Binding Free Energy of Protein and Ligand

    Science.gov (United States)

    Yang, Kun; Wang, Xicheng

    2010-05-01

    Predicting the binding free energy is an important problem in bimolecular simulation. Such prediction would be great benefit in understanding protein functions, and may be useful for computational prediction of ligand binding strengths, e.g., in discovering pharmaceutical drugs. Free energy perturbation (FEP)/thermodynamics integration (TI) is a classical method to explicitly predict free energy. However, this method need plenty of time to collect datum, and that attempts to deal with some simple systems and small changes of molecular structures. Another one for estimating ligand binding affinities is linear interaction energy (LIE) method. This method employs averages of interaction potential energy terms from molecular dynamics simulations or other thermal conformational sampling techniques. Incorporation of systematic deviations from electrostatic linear response, derived from free energy perturbation studies, into the absolute binding free energy expression significantly enhances the accuracy of the approach. However, it also is time-consuming work. In this paper, a new prediction method based on steered molecular dynamics (SMD) with direction optimization is developed to compute binding free energy. Jarzynski's equality is used to derive the PMF or free-energy. The results for two numerical examples are presented, showing that the method has good accuracy and efficiency. The novel method can also simulate whole binding proceeding and give some important structural information about development of new drugs.

  14. Exciton binding energy in GaAsBiN spherical quantum dot heterostructures

    Science.gov (United States)

    Das, Subhasis; Dhar, S.

    2017-03-01

    The ground state exciton binding energies (EBE) of heavy hole excitons in GaAs1-x-yBixNy - GaAs spherical quantum dots (QD) are calculated using a variational approach under 1s hydrogenic wavefunctions within the framework of effective mass approximation. Both the nitrogen and the bismuth content in the material are found to affect the binding energy, in particular for larger nitrogen content and lower dot radii. Calculations also show that the ground state exciton binding energies of heavy holes increase more at smaller dot sizes as compared to that for the light hole excitons.

  15. Binding Energy of Biexcitons in GaAs Quantum-Well Wires

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-Jun; CHEN Xiao-Fang; LI Shu-Shen

    2004-01-01

    @@ The binding energy of a biexciton in GaAs quantum-well wires is calculated variationally by use ofa two-parameter trial wavefunction and a one-dimensional equivalent potential model. There is no artificial parameter added in our calculation. Our results agree fairly well with the previous results. It is found that the binding energies are closely correlative to the size of wire. The binding energy of biexcitons is smaller than that of neutral bound excitons in GaAs quantum-well wires when the dopant is located at the centre of the wires.

  16. On the binding energies of excitons in polar quantum well structures in a weak electric field

    Institute of Scientific and Technical Information of China (English)

    Wu Yun-Feng; Liang Xi-Xia; K. K. Bajaj

    2005-01-01

    The binding energies of excitons in quantum well structures subjected to an applied uniform electric field by taking into account the exciton longitudinal optical phonon interaction is calculated. The binding energies and corresponding Stark shifts for Ⅲ-Ⅴ and Ⅱ-Ⅵ compound semiconductor quantum well structures have been numerically computed.The results for GaAs/AlGaAs and ZnCdSe/ZnSe quantum wells are given and discussed. Theoretical results show that the exciton-phonon coupling reduces both the exciton binding energies and the Stark shifts by screening the Coulomb interaction. This effect is observable experimentally and cannot be neglected.

  17. Subsite binding energies of an exo-polygalacturonase using isothermal titration calorimetry

    Energy Technology Data Exchange (ETDEWEB)

    Mertens, Jeffrey A., E-mail: Jeffrey.Mertens@ars.usda.gov [Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604 (United States); Hector, Ronald E.; Bowman, Michael J. [Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604 (United States)

    2012-01-10

    Highlights: Black-Right-Pointing-Pointer Thermodynamics of (GalpA){sub n} oligomers binding to an exo-polygalacturonase. Black-Right-Pointing-Pointer Energetics of binding (GalpA){sub n} were determined by ITC. Black-Right-Pointing-Pointer Thermodynamic parameters attributable to individual subsites were determined. - Abstract: Thermodynamic parameters for binding of a series of galacturonic acid oligomers to an exo-polygalacturonase, RPG16 from Rhizopus oryzae, were determined by isothermal titration calorimetry. Binding of oligomers varying in chain length from two to five galacturonic acid residues is an exothermic process that is enthalpically driven and results in extremely tight binding of the substrate to RPG16. Binding energies in combination with prior biochemical data suggests that RPG16 has the potential for five subsites, -1 to +4, with the greatest contribution to binding energies arising from subsite -1/+1. While the enthalpic contribution to binding decreases substantially for subsites +2 to +4, beneficial entropic effects occur in subsites +3 and +4 leading to increased total free energy as the length of oligomer increases. This information will be useful for additional studies in determining the binding contributions of specific amino acids with mutant enzymes.

  18. In Silico Docking, Molecular Dynamics and Binding Energy Insights into the Bolinaquinone-Clathrin Terminal Domain Binding Site

    Directory of Open Access Journals (Sweden)

    Mohammed K. Abdel-Hamid

    2014-05-01

    Full Text Available Clathrin-mediated endocytosis (CME is a process that regulates selective internalization of important cellular cargo using clathrin-coated vesicles. Perturbation of this process has been linked to many diseases including cancer and neurodegenerative conditions. Chemical proteomics identified the marine metabolite, 2-hydroxy-5-methoxy-3-(((1S,4aS,8aS-1,4a,5-trimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-2-ylmethylcyclohexa- 2,5-diene-1,4-dione (bolinaquinone as a clathrin inhibitor. While being an attractive medicinal chemistry target, the lack of data about bolinaquinone’s mode of binding to the clathrin enzyme represents a major limitation for its structural optimization. We have used a molecular modeling approach to rationalize the observed activity of bolinaquinone and to predict its mode of binding with the clathrin terminal domain (CTD. The applied protocol started by global rigid-protein docking followed by flexible docking, molecular dynamics and linear interaction energy calculations. The results revealed the potential of bolinaquinone to interact with various pockets within the CTD, including the clathrin-box binding site. The results also highlight the importance of electrostatic contacts over van der Waals interactions for proper binding between bolinaquinone and its possible binding sites. This study provides a novel model that has the potential to allow rapid elaboration of bolinaquinone analogues as a new class of clathrin inhibitors.

  19. Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy.

    Science.gov (United States)

    Payne, Christina M; Jiang, Wei; Shirts, Michael R; Himmel, Michael E; Crowley, Michael F; Beckham, Gregg T

    2013-12-18

    Many glycoside hydrolase (GH) enzymes act via a processive mechanism whereby an individual carbohydrate polymer chain is decrystallized and hydrolyzed along the chain without substrate dissociation. Despite considerable structural and biochemical studies, a molecular-level theory of processivity that relates directly to structural features of GH enzymes does not exist. Here, we hypothesize that the degree of processivity is directly linked to the ability of an enzyme to decrystallize a polymer chain from a crystal, quantified by the binding free energy of the enzyme to the cello-oligosaccharide. We develop a simple mathematical relationship formalizing this hypothesis to quantitatively relate the binding free energy to experimentally measurable kinetic parameters. We then calculate the absolute ligand binding free energy of cellulose chains to the biologically and industrially important GH Family 7 processive cellulases with free energy perturbation/replica-exchange molecular dynamics. Taken with previous observations, our results suggest that degree of processivity is directly correlated to the binding free energy of cello-oligosaccharide ligands to GH7s. The observed binding free energies also suggest candidate polymer morphologies susceptible to enzyme action when compared to the work required to decrystallize cellulose chains. We posit that the ligand binding free energy is a key parameter in comparing the activity and function of GHs and may offer a molecular-level basis toward a general theory of carbohydrate processivity in GHs and other enzymes able to process linear carbohydrate polymers, such as cellulose and chitin synthases.

  20. Fragmentation cross sections and binding energies of neutron-rich nuclei

    Science.gov (United States)

    Tsang, M. B.; Lynch, W. G.; Friedman, W. A.; Mocko, M.; Sun, Z. Y.; Aoi, N.; Cook, J. M.; Delaunay, F.; Famiano, M. A.; Hui, H.; Imai, N.; Iwasaki, H.; Motobayashi, T.; Niikura, M.; Onishi, T.; Rogers, A. M.; Sakurai, H.; Suzuki, H.; Takeshita, E.; Takeuchi, S.; Wallace, M. S.

    2007-10-01

    An exponential dependence of the fragmentation cross section on the average binding energy is observed and reproduced with a statistical model. The observed functional dependence is robust and allows the extraction of binding energies from measured cross sections. From the systematics of Cu isotope cross sections, the binding energies of Cu76,77,78,79 have been extracted. They are 636.94±0.4,647.1±0.4,651.6±0.4, and 657.8±0.5 MeV, respectively. Specifically, the uncertainty of the binding energy of Cu75 is reduced from 980 keV, as listed in the 2003 mass table of Audi, Wapstra, and Thibault to 400 keV. The predicted cross sections of two near drip-line nuclei, Na39 and Mg40 from the fragmentation of Ca48 are discussed.

  1. A general scheme for the estimation of oxygen binding energies on binary transition metal surface alloys

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Nørskov, Jens Kehlet

    2005-01-01

    A simple scheme for the estimation of oxygen binding energies on transition metal surface alloys is presented. It is shown that a d-band center model of the alloy surfaces is a convenient and appropriate basis for this scheme; variations in chemical composition, strain effects, and ligand effects...... for the estimation of oxygen binding energies on a wide variety of transition metal alloys. (c) 2005 Elsevier B.V. All rights reserved....

  2. SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.

    Science.gov (United States)

    Petukh, Marharyta; Dai, Luogeng; Alexov, Emil

    2016-04-12

    Predicting the effect of amino acid substitutions on protein-protein affinity (typically evaluated via the change of protein binding free energy) is important for both understanding the disease-causing mechanism of missense mutations and guiding protein engineering. In addition, researchers are also interested in understanding which energy components are mostly affected by the mutation and how the mutation affects the overall structure of the corresponding protein. Here we report a webserver, the Single Amino Acid Mutation based change in Binding free Energy (SAAMBE) webserver, which addresses the demand for tools for predicting the change of protein binding free energy. SAAMBE is an easy to use webserver, which only requires that a coordinate file be inputted and the user is provided with various, but easy to navigate, options. The user specifies the mutation position, wild type residue and type of mutation to be made. The server predicts the binding free energy change, the changes of the corresponding energy components and provides the energy minimized 3D structure of the wild type and mutant proteins for download. The SAAMBE protocol performance was tested by benchmarking the predictions against over 1300 experimentally determined changes of binding free energy and a Pearson correlation coefficient of 0.62 was obtained. How the predictions can be used for discriminating disease-causing from harmless mutations is discussed. The webserver can be accessed via http://compbio.clemson.edu/saambe_webserver/.

  3. Accurate determination of the binding energy of the formic acid dimer: The importance of geometry relaxation

    Science.gov (United States)

    Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2014-02-01

    The formic acid dimer in its C2h-symmetrical cyclic form is stabilized by two equivalent H-bonds. The currently accepted interaction energy is 18.75 kcal/mol whereas the experimental binding energy D0 value is only 14.22 ±0.12 kcal/mol [F. Kollipost, R. W. Larsen, A. V. Domanskaya, M. Nörenberg, and M. A. Suhm, J. Chem. Phys. 136, 151101 (2012)]. Calculation of the binding energies De and D0 at the CCSD(T) (Coupled Cluster with Single and Double excitations and perturbative Triple excitations)/CBS (Complete Basis Set) level of theory, utilizing CCSD(T)/CBS geometries and the frequencies of the dimer and monomer, reveals that there is a 3.2 kcal/mol difference between interaction energy and binding energy De, which results from (i) not relaxing the geometry of the monomers upon dissociation of the dimer and (ii) approximating CCSD(T) correlation effects with MP2. The most accurate CCSD(T)/CBS values obtained in this work are De = 15.55 and D0 = 14.32 kcal/mol where the latter binding energy differs from the experimental value by 0.1 kcal/mol. The necessity of employing augmented VQZ and VPZ calculations and relaxing monomer geometries of H-bonded complexes upon dissociation to obtain reliable binding energies is emphasized.

  4. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.

    Science.gov (United States)

    Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil

    2013-01-28

    Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder ( http://www.charmm-gui.org/input/gbinding ), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently set up the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three nonpolar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). Therefore, CHARMM-GUI Ligand Binder provides a convenient and reliable way to set up the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems.

  5. Binding energies of nucleobase complexes: Relevance to homology recognition of DNA

    Science.gov (United States)

    León, Sergio Cruz; Prentiss, Mara; Fyta, Maria

    2016-06-01

    The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into the Watson-Crick complexes in order to evaluate the variation in the binding energy with respect to the canonical Watson-Crick pairs. A linear variation of this binding energy with the degree of mismatching is observed. The binding energies for the duplets and triplets containing mismatches are further compared to the energies of the respective singlets in order to assess the degree of collectivity in these complexes. This study also suggests that mismatches do not considerably affect the energetics of canonical base pairs. Our work is highly relevant to the recognition process in DNA promoted through the RecA protein and suggests a clear distinction between recognition in singlets, and recognition in duplets or triplets. Our work assesses the importance of collectivity in the homology recognition of DNA.

  6. Binding Energy of Molecules on Water Ice: Laboratory Measurements and Modeling

    CERN Document Server

    He, Jiao; Vidali, Gianfranco

    2016-01-01

    We measured the binding energy of N$_2$, CO, O$_2$, CH$_4$, and CO$_2$ on non-porous (compact) amorphous solid water (np-ASW), of N$_2$ and CO on porous amorphous solid water (p-ASW), and of NH$_3$ on crystalline water ice. We were able to measure binding energies down to a fraction of 1\\% of a layer, thus making these measurements more appropriate for astrochemistry than the existing values. We found that CO$_2$ forms clusters on np-ASW surface even at very low coverages. The binding energies of N$_2$, CO, O$_2$, and CH$_4$ decrease with coverage in the submonolayer regime. Their values at the low coverage limit are much higher than what is commonly used in gas-grain models. An empirical formula was used to describe the coverage dependence of the binding energies. We used the newly determined binding energy distributions in a simulation of gas-grain chemistry for cold cloud and hot core models. We found that owing to the higher value of desorption energy in the sub-monlayer regime a fraction of all these ice...

  7. Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking.

    Science.gov (United States)

    Minh, David D L

    2012-09-14

    A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor configurations only need to be sampled once, facilitating the use of binding free energy calculations in virtual screening. Demonstrative calculations on a host-guest system yield good agreement with previous free energy calculations and isothermal titration calorimetry measurements. Implicit ligand theory provides guidance on how to improve existing molecular docking algorithms and insight into the concepts of induced fit and conformational selection in noncovalent macromolecular recognition.

  8. Binding Energy of an Off-Center D- in a Spherical Quantum Dot

    Institute of Scientific and Technical Information of China (English)

    LIU Dong-Ming; XIE Wen-Fang

    2009-01-01

    Using the method of matrix diagonalization, we investigate an off-center D- in a spherical quantum dot (QD) subjected to a parabolic potential confinement. We discuss the effect of the position of an impurity in the QD on the binding energy of the D- system. Furthermore, we compare a negatively charged donor D- with a neutral donor D0 confined by a spherical QD with a parabolic potential. The results have dearly demonstrate the so-called quantum size effect. The binding energy/s dependent on the confining potential hω0 and the impurity ion distance D.

  9. Hypernuclear interactions and the binding energies of and hypernuclei

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R.; Usmani, Q.N.

    1988-01-01

    By use of variational calculations a reasonable hadronic description is obtained of the s-shell hypernuclei, of /sub /ZBe, and of the well depth, with N forces which are consistent with p scattering and which are quite strongly spin-dependent, with reasonable TPE NN forces with strongly repulsive dispersive-type NN forces. For the latter we also consider a spin-dependent version which is somewhat favored by our analysis. /sub /ZBe is treated as a 2ed + system and is significantly overbound, approx. =1 MeV, if only ed ed and ed potentials are used. An ed ed potential obtained from the NN forces nicely accounts for this overbinding. The hypernuclei /sub /WHe and /sub / Be are treated as ed + 2 and 2ed + 2 systems. Use of the /sub / Be event gives approx. =1.5 MeV too little binding for /sub /WHe. The S0 potential obtained from /sub / Be is quite strongly attractive, comparable to the N and also to the NN potential without OPE. 18 refs.

  10. Theoretical studies on the binding energy of β-sheet models

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this paper,B3LYP and MP2 methods are used to investigate the binding energy of seventeen antiparallel and parallel β-sheet models. The results indicate that the binding energy obtained from B3LYP calculations is weaker than that obtained from MP2 calculations but the relative binding energy yielded by B3LYP is almost the same as that by MP2. For the antiparallel β-sheets in which two N―H···O═C hydrogen bonds can form either a large hydrogen-bonded ring or a small hydrogen-bonded ring,the binding energy increases obviously when one large ring unit is added,whereas it only changes slightly when one small ring unit is added because of the secondary electrostatic repulsive interaction existing in the small ring unit which is estimated to be about 20 kJ/mol. For the parallel β-sheet models,the binding energy increases almost exactly linearly with the increase of the chain length.

  11. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations.

  12. Binding energies of hypernuclei and. lambda. -nuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R.; Usmani, Q.N.

    1985-01-01

    Variational Monte Carlo calculations have been made for the s-shell hypernuclei and also of /sup 9/Be hypernuclei with a 2..cap alpha.. + ..lambda.. model. The well depth is calculated variationally with the Fermi hypernetted chain method. A satisfactory description of all the relevant experimental ..lambda.. separation energies and also of the ..lambda..p scattering can be obtained with reasonable TPE ..lambda..N and ..lambda..NN forces and strongly repulsive dispersive ..lambda..NN forces which are preferred to be spin dependent. We discuss variational calculations for /sup 6/He and /sup 10/Be hypernuclei with ..cap alpha.. + 2..lambda.. and 2..cap alpha.. + 2..lambda.. models, and the results obtained for the ..lambda lambda.. interaction and for /sup 6/He hypernuclei from analysis of /sup 10/Be hypernuclei Coulomb effects and charge symmetry breaking in the A = 4 hypernuclei are discussed. 24 refs., 5 figs.

  13. Evaluation of atomic electron binding energies for Monte Carlo particle transport

    CERN Document Server

    Pia, Maria Grazia; Batic, Matej; Begalli, Marcia; Kim, Chan Hyeong; Quintieri, Lina; Saracco, Paolo

    2011-01-01

    A survey of atomic binding energies used by general purpose Monte Carlo systems is reported. Various compilations of these parameters have been evaluated; their accuracy is estimated with respect to experimental data. Their effects on physics quantities relevant to Monte Carlo particle transport are highlighted: X-ray fluorescence emission, electron and proton ionization cross sections, and Doppler broadening in Compton scattering. The effects due to different binding energies are quantified with respect to experimental data. The results of the analysis provide quantitative ground for the selection of binding energies to optimize the accuracy of Monte Carlo simulation in experimental use cases. Recommendations on software design dealing with these parameters and on the improvement of data libraries for Monte Carlo simulation are discussed.

  14. Fragmentation cross-sections and binding energies of neutron-rich nuclei

    CERN Document Server

    Tsang, M B; Friedman, W A; Mocko, M; Sun, Z Y; Aoi, N; Cook, J M; Delaunay, F; Famiano, M A; Hui, H; Imai, N; Iwasaki, H; Motobayashi, T; Niikura, M; Onishi, T; Rogers, A M; Sakuraï, H; Suzuki, H; Takeshita, E; Takeuchi, S; Wallace, M S

    2007-01-01

    An exponential dependence of the fragmentation cross-section on the average binding energy is observed and reproduced with a statistical model. The observed functional dependence is robust and allows the extraction of binding energies from measured cross-sections. From the systematics of 75,77,78,79Cu isotope cross-sections have been extracted. They are 636.94 +/- 0.40 MeV, 647.1 +/- 0.4 MeV, 651.6 +/- 0.4 MeV and 657.8 +/- 0.5 MeV, respectively. Specifically, the uncertainty of the binding energy of 75Cu is reduced from 980 keV (listed value in the 2003 mass table of Audi and Wapstra) to 400 keV. The predicted cross-sections of two near drip-line nuclei, 39Na and 40Mg, from the fragmentation of 48Ca are discussed.

  15. Radii and binding energies in oxygen isotopes: a puzzle for nuclear forces

    CERN Document Server

    Lapoux, V; Barbieri, C; Hergert, H; Holt, J D; Stroberg, R

    2016-01-01

    We present a systematic study of both nuclear radii and binding energies in (even) oxygen isotopes from the valley of stability to the neutron drip line. Both charge and matter radii are compared to state-of-the-art {\\it ab initio} calculations along with binding energy systematics. Experimental matter radii are obtained through a complete evaluation of the available elastic proton scattering data of oxygen isotopes. We show that, in spite of a good reproduction of binding energies, {\\it ab initio} calculations with conventional nuclear interactions derived within chiral effective field theory fail to provide a realistic description of charge and matter radii. A novel version of two- and three-nucleon forces leads to considerable improvement of the simultaneous description of the three observables for stable isotopes, but shows deficiencies for the most neutron-rich systems. Thus, crucial challenges related to the development of nuclear interactions remain.

  16. Radii and Binding Energies in Oxygen Isotopes: A Challenge for Nuclear Forces.

    Science.gov (United States)

    Lapoux, V; Somà, V; Barbieri, C; Hergert, H; Holt, J D; Stroberg, S R

    2016-07-29

    We present a systematic study of both nuclear radii and binding energies in (even) oxygen isotopes from the valley of stability to the neutron drip line. Both charge and matter radii are compared to state-of-the-art ab initio calculations along with binding energy systematics. Experimental matter radii are obtained through a complete evaluation of the available elastic proton scattering data of oxygen isotopes. We show that, in spite of a good reproduction of binding energies, ab initio calculations with conventional nuclear interactions derived within chiral effective field theory fail to provide a realistic description of charge and matter radii. A novel version of two- and three-nucleon forces leads to considerable improvement of the simultaneous description of the three observables for stable isotopes but shows deficiencies for the most neutron-rich systems. Thus, crucial challenges related to the development of nuclear interactions remain.

  17. Exciton size and binding energy limitations in one-dimensional organic materials

    Energy Technology Data Exchange (ETDEWEB)

    Kraner, S., E-mail: stefan.kraner@iapp.de; Koerner, C.; Leo, K. [Institut für Angewandte Photophysik, Technische Universität Dresden, Dresden (Germany); Scholz, R. [Institut für Angewandte Photophysik, Technische Universität Dresden, Dresden (Germany); Dresden Center of Computational Materials Science, Technische Universität Dresden, D-01062 Dresden (Germany); Plasser, F. [Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna (Austria)

    2015-12-28

    In current organic photovoltaic devices, the loss in energy caused by the charge transfer step necessary for exciton dissociation leads to a low open circuit voltage, being one of the main reasons for rather low power conversion efficiencies. A possible approach to avoid these losses is to tune the exciton binding energy to a value of the order of thermal energy, which would lead to free charges upon absorption of a photon, and therefore increase the power conversion efficiency towards the Shockley-Queisser limit. We determine the size of the excitons for different organic molecules and polymers by time dependent density functional theory calculations. For optically relevant transitions, the exciton size saturates around 0.7 nm for one-dimensional molecules with a size longer than about 4 nm. For the ladder-type polymer poly(benzimidazobenzophenanthroline), we obtain an exciton binding energy of about 0.3 eV, serving as a lower limit of the exciton binding energy for the organic materials investigated. Furthermore, we show that charge transfer transitions increase the exciton size and thus identify possible routes towards a further decrease of the exciton binding energy.

  18. Distribution of binding energies of a water molecule in the water liquid-vapor interface

    Energy Technology Data Exchange (ETDEWEB)

    Chempath, Shaji [Los Alamos National Laboratory; Pratt, Lawrence R [TULANE UNIV

    2008-01-01

    Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

  19. Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions.

    Science.gov (United States)

    Singh, Nidhi; Warshel, Arieh

    2010-05-15

    Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer-aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic linear response approximation (LRA/beta version) and related approaches including the linear interaction energy (LIE) to the more approximated and considerably faster scaled protein dipoles Langevin dipoles (PDLD/S-LRA version) as well as the less rigorous molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA) and generalized born/surface area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/beta, the LIE, the PDLD/S-LRA/beta, and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the nonelectrostatic term. The PDLD/S-LRA/beta performs effectively without the need of reparameterization. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies because of its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S-LRA/beta appears to offer an appealing option for the final stages of massive screening approaches.

  20. Protein:Ligand binding free energies: A stringent test for computational protein design.

    Science.gov (United States)

    Druart, Karen; Palmai, Zoltan; Omarjee, Eyaz; Simonson, Thomas

    2016-02-01

    A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl-tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l-tyrosine (l-Tyr), compared to the analogs d-Tyr, p-acetyl-, and p-azido-phenylalanine (ac-Phe, az-Phe). We simulate l- and d-Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous "MD/GBSA" procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l-Tyr, ac- and az-Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l-Tyr or d-Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l-Tyr is the ligand and a d-Tyr specific mutant when d-Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln.

  1. Does alpha-helix folding necessarily provide an energy source for the protein-lipid binding?

    Science.gov (United States)

    Gursky, Olga

    2007-01-01

    Lipid-induced alpha-helix folding, which occurs in many lipid surface-binding proteins and peptides such as apolipoproteins and synucleins, has been proposed to provide an energy source for protein-lipid interactions. We propose that in a system comprised of a phospholipid surface and a small polypeptide that is unfolded in solution and binds reversibly to lipid surface, helical folding involves expenditure of free energy as compared to a similar polypeptide that is alpha-helical in solution. This is a consequence of the entropic cost of helix folding that is illustrated in a simple thermodynamic model and exemplifies the general "key-into-lock" paradigm of protein-ligand binding. Even though this simple model does not explicitly address the protein-induced lipid re-arrangement and may not directly apply to large proteins that undergo significant tertiary structural changes upon lipid binding, it suggests that the notion of helix folding as an energy source for lipid binding should be treated with caution.

  2. Structural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers by in silico molecular docking, molecular dynamics, and binding free energy calculations.

    Science.gov (United States)

    Tripathi, Shubhandra; Kumar, Akhil; Kumar, B Sathish; Negi, Arvind S; Sharma, Ashok

    2016-06-01

    Microtubule stabilizers provide an important mode of treatment via mitotic cell arrest of cancer cells. Recently, we reported two novel neolignans derivatives Cmp10 and Cmp19 showing anticancer activity and working as microtubule stabilizers at micromolar concentrations. In this study, we have explored the binding site, mode of binding, and stabilization by two novel microtubule stabilizers Cmp10 and Cmp19 using in silico molecular docking, molecular dynamics (MD) simulation, and binding free energy calculations. Molecular docking studies were performed to explore the β-tubulin binding site of Cmp10 and Cmp19. Further, MD simulations were used to probe the β-tubulin stabilization mechanism by Cmp10 and Cmp19. Binding affinity was also compared for Cmp10 and Cmp19 using binding free energy calculations. Our docking results revealed that both the compounds bind at Ptxl binding site in β-tubulin. MD simulation studies showed that Cmp10 and Cmp19 binding stabilizes M-loop (Phe272-Val288) residues of β-tubulin and prevent its dynamics, leading to a better packing between α and β subunits from adjacent tubulin dimers. In addition, His229, Ser280 and Gln281, and Arg278, Thr276, and Ser232 were found to be the key amino acid residues forming H-bonds with Cmp10 and Cmp19, respectively. Consequently, binding free energy calculations indicated that Cmp10 (-113.655 kJ/mol) had better binding compared to Cmp19 (-95.216 kJ/mol). This study provides useful insight for better understanding of the binding mechanism of Cmp10 and Cmp19 and will be helpful in designing novel microtubule stabilizers.

  3. Modeling the chemical shift of lanthanide 4f electron binding energies

    NARCIS (Netherlands)

    Dorenbos, P.

    2012-01-01

    Lanthanides in compounds can adopt the tetravalent [Xe]4fn−1 (like Ce4+, Pr4+, Tb4+), the trivalent [Xe]4fn (all lanthanides), or the divalent [Xe]4f n+1 configuration (like Eu2+, Yb2+, Sm2+, Tm2+). The 4f-electron binding energy depends on the charge Q of the lanthanide ion and its chemical environ

  4. Comparison of experimental and theoretical binding and transition energies in the actinide region. [Review

    Energy Technology Data Exchange (ETDEWEB)

    Krause, M.O.; Nestor, C.W. Jr.

    1977-01-01

    The status of experimental and theoretical binding and transition energy determinations is reviewed extending the comparison between experiment and theory to encompass representative series of data for all actinides. This comprehensive comparison reveals areas where improvements may be indicated, showing whether theoretical treatments including all known contributions to the lowest order would be adequate in all instances. 45 references. (JFP)

  5. Increased binding energy of impurities near a semiconductor-vacuum interface

    Energy Technology Data Exchange (ETDEWEB)

    Wijnheijmer, A.P.; Garleff, J.K.; Koenraad, P.M. [PSN, Eindhoven University of Technology (Netherlands); Teichmann, K.; Wenderoth, M.; Loth, S.; Ulbrich, R.G. [IV. Phys. Inst., Georg-August Univ. Goettingen (Germany)

    2008-07-01

    We have recently shown that a STM tip can be used as a tool to manipulate the charge state of individual impurities below the cleavage surface of a semiconductor. This manipulation allowed us to determine the binding energy of single donors and acceptors as a function of their depth (up to 1 nm) below the surface. We found that the binding energy strongly increases near the surface. In the case of a Si-donor in GaAs the binding energy increases continuously from 5.6 meV in the bulk to about 150 meV close to the surface. Our STM techniques also allowed for the determination of the size and shape of the Coulomb field of single ionized donors. We found that the range of the potential is strongly reduced relative to the bulk value. Both the reduced range of the Coulomb potential and the increased binding energy can be related to a reduced dielectric constant and increased effective mass near the surface. We discuss the implications of these findings.

  6. A new interpretation of the proton-neutron bound state The calculation of the binding energy

    CERN Document Server

    Mandache, N

    1996-01-01

    We treat the old problem of the proton-neutron bound state (the deuteron). Using a new concept of incomplete (partial) annihilation process we derive a formula for the binding energy of the deuteron, which does not contain any new constant. Some implications of this new approach are discussed.

  7. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

    Science.gov (United States)

    Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

    2016-06-30

    In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  8. Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes.

    Science.gov (United States)

    Miranda, Williams E; Noskov, Sergei Yu; Valiente, Pedro A

    2015-09-28

    In this work, we introduced an improved linear interaction energy (LIE) method parameterization for computations of protein–ligand binding free energies. The protocol, coined LIE-D, builds on the linear relationship between the empirical coefficient γ in the standard LIE scheme and the D parameter, introduced in our work. The D-parameter encompasses the balance (difference) between electrostatic (polar) and van der Waals (nonpolar) energies in protein–ligand complexes. Leave-one-out cross-validation showed that LIE-D reproduced accurately the absolute binding free energies for our training set of protein–ligand complexes ( = 0.92 kcal/mol, SDerror = 0.66 kcal/mol, R(2) = 0.90, QLOO(2) = 0.89, and sPRESS(LOO) = 1.28 kcal/mol). We also demonstrated LIE-D robustness by predicting accurately the binding free energies for three different protein–ligand systems outside the training data set, where the electrostatic and van der Waals interaction energies were calculated with different force fields.

  9. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

    Science.gov (United States)

    Jiang, Wei; Roux, Benoît

    2010-07-01

    Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

  10. Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics

    Science.gov (United States)

    Bhakat, Soumendranath; Söderhjelm, Pär

    2017-01-01

    The funnel metadynamics method enables rigorous calculation of the potential of mean force along an arbitrary binding path and thereby evaluation of the absolute binding free energy. A problem of such physical paths is that the mechanism characterizing the binding process is not always obvious. In particular, it might involve reorganization of the solvent in the binding site, which is not easily captured with a few geometrically defined collective variables that can be used for biasing. In this paper, we propose and test a simple method to resolve this trapped-water problem by dividing the process into an artificial host-desolvation step and an actual binding step. We show that, under certain circumstances, the contribution from the desolvation step can be calculated without introducing further statistical errors. We apply the method to the problem of predicting host-guest binding free energies in the SAMPL5 blind challenge, using two octa-acid hosts and six guest molecules. For one of the hosts, well-converged results are obtained and the prediction of relative binding free energies is the best among all the SAMPL5 submissions. For the other host, which has a narrower binding pocket, the statistical uncertainties are slightly higher; longer simulations would therefore be needed to obtain conclusive results.

  11. Precision Measurement of the 29Si, 33S, and 36Cl Binding Energies

    CERN Document Server

    Dewey, M S; Deslattes, R D; Doll, C; Jentschel, M; Mutti, P

    2006-01-01

    The binding energies of 29Si, 33S, and 36Cl have been measured with a relative uncertainty $< 0.59 \\times 10^{-6}$ using a flat-crystal spectrometer. The unique features of these measurements are 1) nearly perfect crystals whose lattice spacing is known in meters, 2) a highly precise angle scale that is derived from first principles, and 3) a gamma-ray measurement facility that is coupled to a high flux reactor with near-core source capability. The binding energy is obtained by measuring all gamma-rays in a cascade scheme connecting the capture and ground states. The measurements require the extension of precision flat-crystal diffraction techniques to the 5 to 6 MeV energy region, a significant precision measurement challenge. The binding energies determined from these gamma-ray measurements are consistent with recent highly accurate atomic mass measurements within a relative uncertainty of $4.3 \\times 10^{-7}$. The gamma-ray measurement uncertainties are the dominant contributors to the uncertainty of th...

  12. Assessment of Density Functional Methods for Exciton Binding Energies and Related Optoelectronic Properties

    CERN Document Server

    Lee, Jui-Che; Lin, Shiang-Tai

    2015-01-01

    The exciton binding energy, the energy required to dissociate an excited electron-hole pair into free charge carriers, is one of the key factors to the optoelectronic performance of organic materials. However, it remains unclear whether modern quantum-mechanical calculations, mostly based on Kohn-Sham density functional theory (KS-DFT) and time-dependent density functional theory (TDDFT), are reliably accurate for exciton binding energies. In this study, the exciton binding energies and related optoelectronic properties (e.g., the ionization potentials, electron affinities, fundamental gaps, and optical gaps) of 121 small- to medium-sized molecules are calculated using KS-DFT and TDDFT with various density functionals. Our KS-DFT and TDDFT results are compared with those calculated using highly accurate CCSD and EOM-CCSD methods, respectively. The omegaB97, omegaB97X, and omegaB97X-D functionals are shown to generally outperform (with a mean absolute error of 0.36 eV) other functionals for the properties inve...

  13. Free-energy analysis of enzyme-inhibitor binding: aspartic proteinase-pepstatin complexes.

    Science.gov (United States)

    Kalra, P; Das, A; Jayaram, B

    2001-01-01

    Expeditious in silico determinations of the free energies of binding of a series of inhibitors to an enzyme are of immense practical value in structure-based drug design efforts. Some recent advances in the field of computational chemistry have rendered a rigorous thermodynamic treatment of biologic molecules feasible, starting from a molecular description of the biomolecule, solvent, and salt. Pursuing the goal of developing and making available a software for assessing binding affinities, we present here a computationally rapid, albeit elaborate, methodology to estimate and analyze the molecular thermodynamics of enzyme-inhibitor binding with crystal structures as the point of departure. The complexes of aspartic proteinases with seven inhibitors have been adopted for this study. The standard free energy of complexation is considered in terms of a thermodynamic cycle of six distinct steps decomposed into a total of 18 well-defined components. The model we employed involves explicit all-atom accounts of the energetics of electrostatic interactions, solvent screening effects, van der Waals components, and cavitation effects of solvation combined with a Debye-Huckel treatment of salt effects. The magnitudes and signs of the various components are estimated using the AMBER parm94 force field, generalized Born theory, and solvent accessibility measures. Estimates of translational and rotational entropy losses on complexation as well as corresponding changes in the vibrational and configurational entropy are also included. The calculated standard free energies of binding at this stage are within an order of magnitude of the observed inhibition constants and necessitate further improvements in the computational protocols to enable quantitative predictions. Some areas such as inclusion of structural adaptation effects, incorporation of site-dependent amino acid pKa shifts, consideration of the dynamics of the active site for fine-tuning the methodology are easily

  14. Orbital momentum profiles and binding energy spectra for the complete valence shell of molecular fluorine

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y.; Brion, C.E. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Chemistry; Brunger, M.J.; Zhao, K.; Grisogono, A.M.; Braidwood, S.; Weigold, E. [Flinders Univ. of South Australia, Adelaide, SA (Australia). Electronic Structure of Materials Centre; Chakravorty, S.J.; Davidson, E.R. [Indiana Univ., Bloomington, IN (United States). Dept. of Chemistry; Sgamellotti, A. [Univ di Perugia (Italy). Dipartimento di Chimica; von Niessen, W. [Technische Univ. Braunschweig (Germany). Inst fuer Physikalische

    1996-01-01

    The first electronic structural study of the complete valence shell binding energy spectrum of molecular fluorine, encompassing both the outer and inner valence regions, is reported. These binding energy spectra as well as the individual orbital momentum profiles have been measured using an energy dispersive multichannel electron momentum spectrometer at a total energy of 1500 eV, with an energy resolution of 1.5 eV and a momentum resolution of 0.1 a.u. The measured binding energy spectra in the energy range of 14-60 eV are compared with the results of ADC(4) many-body Green`s function and also direct-Configuration Interaction (CI) and MRSD-CI calculations. The experimental orbital electron momentum profiles are compared with SCF theoretical profiles calculated using the target Hartree-Fock approximation with a range of basis sets and with Density Functional Theory predictions in the target Kohn-Sham approximation with non-local potentials. The truncated (aug-cc-pv5z) Dunning basis sets were used for the Density Functional Theory calculations which also include some treatment of correlation via the exchange and correlation potentials. Comparisons are also made with the full ion-neutral overlap amplitude calculated with MRSD-CI wave functions. Large, saturated basis sets (199-GTO) were employed for both the high level SCF near Hartree-Fock limit and MRSD-CI calculations to investigate the effects of electron correlation and relaxation. 66 refs., 9 tabs., 9 figs.

  15. Calculation of positron binding energies using the generalized any particle propagator theory

    Energy Technology Data Exchange (ETDEWEB)

    Romero, Jonathan; Charry, Jorge A. [Department of Chemistry, Universidad Nacional de Colombia, Av. Cra. 30 #45-03, Bogotá (Colombia); Flores-Moreno, Roberto [Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal., C. P. 44430 (Mexico); Varella, Márcio T. do N. [Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP (Brazil); Reyes, Andrés, E-mail: areyesv@unal.edu.co [Department of Chemistry, Universidad Nacional de Colombia, Av. Cra. 30 #45-03, Bogotá (Colombia); Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP (Brazil)

    2014-09-21

    We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ∼0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.

  16. Calculation of positron binding energies using the generalized any particle propagator theory

    Science.gov (United States)

    Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Márcio T. do N.; Reyes, Andrés

    2014-09-01

    We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ˜0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.

  17. Self-consistent determination of fullerene binding energies BE (C+n-C2), n=58ṡ ṡ ṡ44

    Science.gov (United States)

    Wörgötter, R.; Dünser, B.; Scheier, P.; Märk, T. D.; Foltin, M.; Klots, C. E.; Laskin, J.; Lifshitz, C.

    1996-01-01

    Using recently measured accurate relative partial ionization cross section functions for production of the C60 fragment ions C+58 through C+44 by electron impact ionization, we have determined the respective binding energies BE(C+n-C2), with n=58,...,44, using a novel self-consistent procedure. Appearance energies were determined from ionization efficiency curves. Binding energies were calculated from the corresponding appearance energies with the help of the finite heat bath theory. Then using these binding energies we calculated with transition state theory (TST), the corresponding breakdown curves, and compared these calculated ones with the ones derived from the measured cross sections. The good agreement between these breakdown curves proves the consistency of this multistep calculation scheme. As the only free parameter in this procedure is the binding energy C+58-C2, we studied the influence of different transition states chosen in the determination of this binding energy via TST theory and iterative comparison with breakdown curve measurements. Based on this study we can conclude that extremely loose transition states can be confidently excluded, and that somewhat looser transition states than those used earlier result in an upward change of the binding energy of less than 10% yielding an upper limit for the binding energy C+58-C2 of approximately 7.6 eV.

  18. Excitonic fine structure and binding energies of excitonic complexes in single InAs quantum dashes

    Science.gov (United States)

    Mrowiński, P.; Zieliński, M.; Świderski, M.; Misiewicz, J.; Somers, A.; Reithmaier, J. P.; Höfling, S.; Sek, G.

    2016-09-01

    The fundamental electronic and optical properties of elongated InAs nanostructures embedded in quaternary InGaAlAs barrier are investigated by means of high-resolution optical spectroscopy and many-body atomistic tight-binding theory. These wire-like shaped, self-assembled nanostructures are known as quantum dashes and are typically formed during the molecular beam epitaxial growth on InP substrates. In this paper, we study properties of excitonic complexes confined in quantum dashes emitting in a broad spectral range from below 1.2 to 1.55 μm. We find peculiar trends for the biexciton and negative trion binding energies, with pronounced trion binding in smaller size quantum dashes. These experimental findings are then compared and qualitatively explained by atomistic theory. The theoretical analysis shows a fundamental role of correlation effects for the absolute values of excitonic binding energies. Eventually, we determine the bright exciton fine structure splitting (FSS), where both the experiment and theory predict a broad distribution of the splitting varying from below 50 to almost 180 μeV. We identify several key factors determining the FSS values in such nanostructures, including quantum dash size variation and composition fluctuations.

  19. Modelling of binding free energy of targeted nanocarriers to cell surface

    Science.gov (United States)

    Liu, Jin; Ayyaswamy, Portonovo S.; Eckmann, David M.; Radhakrishnan, Ravi

    2014-03-01

    We have developed a numerical model based on Metropolis Monte Carlo and the weighted histogram analysis method that enables the calculation of the absolute binding free energy between functionalized nanocarriers (NC) and endothelial cell (EC) surfaces. The binding affinities are calculated according to the free energy landscapes. The model predictions quantitatively agree with the analogous measurements of specific antibody coated NCs (100 nm in diameter) to intracellular adhesion molecule-1 (ICAM-1) expressing EC surface in in vitro cell culture experiments. The model also enables an investigation of the effects of a broad range of parameters that include antibody surface coverage of NC, glycocalyx in both in vivo and in vitro conditions, shear flow and NC size. Using our model we explore the effects of shear flow and reproduce the shear-enhanced binding observed in equilibrium measurements in collagen-coated tube. Furthermore, our results indicate that the bond stiffness, representing the specific antibody-antigen interaction, significantly impacts the binding affinities. The predictive success of our computational protocol represents a sound quantitative approach for model driven design and optimization of functionalized NC in targeted vascular drug delivery.

  20. Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids

    Science.gov (United States)

    Anatole von Lilienfeld, O.; Tkatchenko, Alexandre

    2010-06-01

    We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C6 and C9, are computed "on the fly" from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C60 dimer, a peptide (Ala10), an intercalated drug-DNA model [ellipticine-d(CG)2], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.

  1. Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2.

    Science.gov (United States)

    Satpati, Priyadarshi; Clavaguéra, Carine; Ohanessian, Gilles; Simonson, Thomas

    2011-05-26

    Archaeal initiation factor 2 (aIF2) is a protein involved in the initiation of protein biosynthesis. In its GTP-bound, "ON" conformation, aIF2 binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, "OFF" conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and its dependence on the ON or OFF conformational state of aIF2, molecular dynamics free energy simulations (MDFE) are a tool of choice. However, the validity of the computed free energies depends on the simulation model, including the force field and the boundary conditions, and on the extent of conformational sampling in the simulations. aIF2 and other GTPases present specific difficulties; in particular, the nucleotide ligand coordinates a divalent Mg(2+) ion, which can polarize the electronic distribution of its environment. Thus, a force field with an explicit treatment of electronic polarizability could be necessary, rather than a simpler, fixed charge force field. Here, we begin by comparing a fixed charge force field to quantum chemical calculations and experiment for Mg(2+):phosphate binding in solution, with the force field giving large errors. Next, we consider GTP and GDP bound to aIF2 and we compare two fixed charge force fields to the recent, polarizable, AMOEBA force field, extended here in a simple, approximate manner to include GTP. We focus on a quantity that approximates the free energy to change GTP into GDP. Despite the errors seen for Mg(2+):phosphate binding in solution, we observe a substantial cancellation of errors when we compare the free energy change in the protein to that in solution, or when we compare the protein ON and OFF states. Finally, we have used the fixed charge force field to perform MDFE simulations and alchemically transform GTP into GDP in the protein and in solution. With a total of about 200 ns of molecular dynamics, we obtain good convergence and a reasonable statistical uncertainty, comparable to the force

  2. Simulative Calculation of Mechanical Property, Binding Energy and Detonation Property of TATB/Fluorine-polymer PBX

    Institute of Scientific and Technical Information of China (English)

    MA, Xiu-Fang; XIAO, Ji-Jun; HUANG, Hui; JU, Xue-Hai; LI, Jin-Shan; XIAO, He-Ming

    2006-01-01

    Molecular dynamics (MD) method was used to simulate 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) coated with fluorine containing polymers. The mechanical properties and binding energies of PBXs were obtained. It was found that when the number of chain monomers of fluorine containing polymers was the same, the elasticity of TATB/F2314 was increased more greatly than others and the binding energy of TATB/F2311 was the largest among four PBXs. Detonation heat and velocity of such four PBXs were calculated according to theoretical and empirical formulas. The results show that the order of detonation heat is TATB>TATB/PVDF>TATB/F2311 >TATB/F2314>TATB/PCTFE while the order of detonation velocity is TATB/PVDF<TATB/F2311 <TATB/F2314<TATB/PCTFE<TATB.

  3. On the release of binding energy and accretion power in core collapse-like environments

    CERN Document Server

    Socrates, Aristotle

    2008-01-01

    All accretion models of gamma-ray bursts share a common assumption: accretion power and gravitational binding energy is released and then dissipated locally, with the mass of its origin. This is equivalent to the Shakura-Sunyaev 1973 (SS73) prescription for the dissipation of accretion power and subsequent conversion into radiate output. Since their seminal paper, broadband observations of quasars and black hole X-ray binaries insist that the SS73 prescription cannot wholly describe their behavior. In particular, optically thick black hole accretion flows are almost universally accompanied by coronae whose relative power by far exceeds anything seen in studies of stellar chromospheric and coronal activity. In this note, we briefly discuss the possible repercussions of freeing accretion models of GRBs from the SS73 prescription. Our main conclusion is that the efficiency of converting gravitational binding energy into a GRB power can be increased by an order of magnitude or more.

  4. Binding Energy of an Exciton in the Quantum Dot Under a Magnetic Field

    Institute of Scientific and Technical Information of China (English)

    XIE Wen-nng

    2001-01-01

    The author reports on a calculation of the binding energy of the ground and some excited states of excitons in parabolic quantum dots in the presence of an external magnetic field. Calculations are made by using the method of few-body physics within the effective-mass approximation. The results are obtained for several strength values of the magnetic field as a function of the quantum dot radius.

  5. Binding energies of an exciton in a Gaussian potential quantum dot

    Institute of Scientific and Technical Information of China (English)

    Xie Wen-Fang

    2006-01-01

    In this paper, an exciton trapped by a Gaussian confining potential quantum dot has been investigated. Calculations are made by using the method of numerical diagonalization of Hamiltonian in the effective-mass approximation. The dependences of binding energies of the ground state and the first excited state on the size of the confining potential and the strength of the magnetic field are analysed explicitly.

  6. Exciton Binding energies and effective masses in Organo-lead Tri-Halide Perovskites

    Science.gov (United States)

    Portugall, Oliver; Miyata, Atsuhiko; Mitioglu, Anatol; Plochocka, Paulina; Wang, Jacob Tse-Wei; Stranks, Samuel; Snaith, Henry; Nicholas, Robin; Lncmi Toulouse Team; Oxford University Team

    2015-03-01

    Solid-state perovskite-based solar cells have made a dramatic impact on emerging PV research with efficiencies of over 17% already achieved. However, to date the basic electronic properties of the perovskites such as the electron and hole effective masses and the exciton binding energy are not well known. We have measured both for methyl ammonium lead tri-iodide using magneto absorption in very high magnetic fields up to 150T showing that the exciton binding energy at low temperatures is only 16 meV, a value three times smaller than previously thought and sufficiently small to completely transform the way in which the devices must operate. Landau level spectroscopy shows that the reduced effective mass of 0.104 me is also smaller than previously thought. In addition by using a fast pulse 150T magnet we measure the band structure change due to the structural phase transition that occurs in this system at around 160K. We also observe Landau levels in the high temperature phase as used for device production, which has a very similar effective mass and the analysis suggests an exciton binding energy which is even smaller than in the low temperature phase.

  7. Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

    Directory of Open Access Journals (Sweden)

    Bodee Nutho

    2014-11-01

    Full Text Available In the present study, our aim is to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD simulations and binding free energy calculations. The molecular docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the β-CD cavity, whilst less binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/β-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system.

  8. Binding energy of exciton in a nanowire superlattice in magnetic and electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Galvan-Moya, J E; Gutierrez, W [Escuela de Fisica, Universidad Industrial de Santander, Bucaramanga, Colombia A.A. 678 (Colombia); Moscoso, C, E-mail: edogalvan@gmail.co [Departamento de Fisica, Universidad Nacional de Colombia, Bogota, Colombia A.A. 5997 (Colombia)

    2010-02-01

    We study the binding energy of excitons in a cylindrical GaAs/Ga{sub 1-x}Al{sub x}As nanowire superlattice, embedded in Ga{sub 1-y}Al{sub y}As matrix, in the presence of magnetic and electric fields applied parallel to the growth direction. We express the exciton trial function as a product of one-particle wave functions of the electron and the hole with variationally determined envelope function, which describes the exciton intrinsic properties and depends only on the electron-hole separation. By using a functional derivative technique, we derive a differential equation for this envelope function, which we solve numerically. By varying the wire radius, interwell barrier width and well sizes we obtain binding energies ranging in character from one for strongly coupled superlattice to that for a system of stack of isolated disks. The behaviour of the binding energies and the charge distributions as functions of the interwell coupling, well sizes, and the external fields is consistently described with our simple formalism.

  9. First-principles calculation of core-level binding energy shift in surface chemical processes

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Combined with third generation synchrotron radiation light sources, X-ray photoelectron spectroscopy (XPS) with higher energy resolution, brilliance, enhanced surface sensitivity and photoemission cross section in real time found extensive applications in solid-gas interface chemistry. This paper reports the calculation of the core-level binding energy shifts (CLS) using the first-principles density functional theory. The interplay between the CLS calculations and XPS measurements to uncover the structures, adsorption sites and chemical reactions in complex surface chemical processes are highlight. Its application on clean low index (111) and vicinal transition metal surfaces, molecular adsorption in terms of sites and configuration, and reaction kinetics are domonstrated.

  10. Formation Mechanism and Binding Energy for Body-Centered Cubic Structure of He+9 Cluster

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jian-Ping; GOU Qing-Quan; LI Ping

    2004-01-01

    The formation mechanism for the body-centered cubic structure of He+9 cluster is proposed and its total energy curve is calculated by the method of a Modified Arrangement Channel Quantum Mechanics. The energy is the function of separation R between the nuclei at the center and an apex of the body-centered cubic structure. The result of the calculation shows that the curve has a minimal energy -25.6669 (a.u.) at R = 2.550ao. The binding energy of He+9 with respect to He+ + 8He was calculated to be 0.8857 a.u. This means that the cluster of He+9 may be formed in the body-centered cubic structure of R = 2.55a0.

  11. Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.

    Science.gov (United States)

    Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D; Schafer, Nicholas P; Kim, Bobby L; Cheung, Margaret S; Wolynes, Peter G

    2016-01-01

    While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes.

  12. Design of protein-ligand binding based on the molecular-mechanics energy model.

    Science.gov (United States)

    Boas, F Edward; Harbury, Pehr B

    2008-07-04

    While the molecular-mechanics field has standardized on a few potential energy functions, computational protein design efforts are based on potentials that are unique to individual laboratories. Here we show that a standard molecular-mechanics potential energy function without any modifications can be used to engineer protein-ligand binding. A molecular-mechanics potential is used to reconstruct the coordinates of various binding sites with an average root-mean-square error of 0.61 A and to reproduce known ligand-induced side-chain conformational shifts. Within a series of 34 mutants, the calculation can always distinguish between weak (K(d)>1 mM) and tight (K(d)mechanics potential is used to redesign a ribose-binding site. Out of a search space of 2 x 10(12) sequences, the calculation selects a point mutant of the native protein as the top solution (experimental K(d)=17 microM) and the native protein as the second best solution (experimental K(d)=210 nM). The quality of the predictions depends on the accuracy of the generalized Born electrostatics model, treatment of protonation equilibria, high-resolution rotamer sampling, a final local energy minimization step, and explicit modeling of the bound, unbound, and unfolded states. The application of unmodified molecular-mechanics potentials to protein design links two fields in a mutually beneficial way. Design provides a new avenue for testing molecular-mechanics energy functions, and future improvements in these energy functions will presumably lead to more accurate design results.

  13. Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.

    Science.gov (United States)

    Chakavorty, Arghya; Li, Lin; Alexov, Emil

    2016-10-30

    Macromolecular interactions are essential for understanding numerous biological processes and are typically characterized by the binding free energy. Important component of the binding free energy is the electrostatics, which is frequently modeled via the solutions of the Poisson-Boltzmann Equations (PBE). However, numerous works have shown that the electrostatic component (ΔΔGelec ) of binding free energy is very sensitive to the parameters used and modeling protocol. This prompted some researchers to question the robustness of PBE in predicting ΔΔGelec . We argue that the sensitivity of the absolute ΔΔGelec calculated with PBE using different input parameters and definitions does not indicate PBE deficiency, rather this is what should be expected. We show how the apparent sensitivity should be interpreted in terms of the underlying changes in several numerous and physical parameters. We demonstrate that PBE approach is robust within each considered force field (CHARMM-27, AMBER-94, and OPLS-AA) once the corresponding structures are energy minimized. This observation holds despite of using two different molecular surface definitions, pointing again that PBE delivers consistent results within particular force field. The fact that PBE delivered ΔΔGelec values may differ if calculated with different modeling protocols is not a deficiency of PBE, but natural results of the differences of the force field parameters and potential functions for energy minimization. In addition, while the absolute ΔΔGelec values calculated with different force field differ, their ordering remains practically the same allowing for consistent ranking despite of the force field used. © 2016 Wiley Periodicals, Inc.

  14. Absolute binding free energies for octa-acids and guests in SAMPL5

    Science.gov (United States)

    Tofoleanu, Florentina; Lee, Juyong; Pickard, Frank C., IV; König, Gerhard; Huang, Jing; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

    2017-01-01

    As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid (OAMe). We use the double decoupling method via thermodynamic integration (TI) or Hamiltonian replica exchange in connection with the Bennett acceptance ratio (HREM-BAR). We produce the binding poses either through manual docking or by using GalaxyDock-HG, a docking software developed specifically for this study. The root mean square deviations for our most accurate predictions are 1.4 kcal mol-1 for OAH with TI and 1.9 kcal mol-1 for OAMe with HREM-BAR. Our best results for OAMe were obtained for systems with ionic concentrations corresponding to the ionic strength of the experimental solution. The most problematic system contains a halogenated guest. Our attempt to model the σ-hole of the bromine using a constrained off-site point charge, does not improve results. We use results from molecular dynamics simulations to argue that the distinct binding affinities of this guest to OAH and OAMe are due to a difference in the flexibility of the host. We believe that the results of this extensive analysis of host-guest complexes will help improve the protocol used in predicting binding affinities for larger systems, such as protein-substrate compounds.

  15. Locating Temporal Functional Dynamics of Visual Short-Term Memory Binding using Graph Modular Dirichlet Energy

    Science.gov (United States)

    Smith, Keith; Ricaud, Benjamin; Shahid, Nauman; Rhodes, Stephen; Starr, John M.; Ibáñez, Augustin; Parra, Mario A.; Escudero, Javier; Vandergheynst, Pierre

    2017-02-01

    Visual short-term memory binding tasks are a promising early marker for Alzheimer’s disease (AD). To uncover functional deficits of AD in these tasks it is meaningful to first study unimpaired brain function. Electroencephalogram recordings were obtained from encoding and maintenance periods of tasks performed by healthy young volunteers. We probe the task’s transient physiological underpinnings by contrasting shape only (Shape) and shape-colour binding (Bind) conditions, displayed in the left and right sides of the screen, separately. Particularly, we introduce and implement a novel technique named Modular Dirichlet Energy (MDE) which allows robust and flexible analysis of the functional network with unprecedented temporal precision. We find that connectivity in the Bind condition is less integrated with the global network than in the Shape condition in occipital and frontal modules during the encoding period of the right screen condition. Using MDE we are able to discern driving effects in the occipital module between 100–140 ms, coinciding with the P100 visually evoked potential, followed by a driving effect in the frontal module between 140–180 ms, suggesting that the differences found constitute an information processing difference between these modules. This provides temporally precise information over a heterogeneous population in promising tasks for the detection of AD.

  16. Two and three-body interatomic dispersion energy contributions to binding in molecules and solids

    Science.gov (United States)

    von Lilienfeld, Anatole; Tkatchenko, Alexandre

    2010-03-01

    Numerical estimates of the leading two and three body dispersion energy terms in van der Waals (vdW) interactions are presented for a broad variety of molecules and solids. The calculations employ London and Axilrod-Teller-Muto expressions damped at short interatomic distances, where the required interatomic dispersion energy coefficients, C6 and C9, are computed from first-principles. The investigated systems include the S22 database of non-covalent interactions, benzene and ice crystals, bilayer graphene, fullerene dimer, a poly peptide (Ala10), an intercalated drug-DNA model (Ellipticine-d(CG)2), 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and molecular crystals from a crystal structure blind test. We find that the 2 and 3-body interatomic dispersion energies contribute significantly to binding and cohesive energies, for some systems they can reach up to 50% of experimental estimates of absolute binding. Our results suggest that interatomic 3-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.

  17. Binding Energy of an Exciton Bound to Ionized Acceptor in Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    XIE Wen-Fang

    2001-01-01

    Binding energiesfor an exciton (X ) trapped in the two-dimensional quantum dot by a negative ion located on the z axis at a distance from the dot plane are calculated by using the method of few-body physics.This configuration is called a barrier (A-,X) center.The dependence of the binding energy of the ground state of the barrier (A-,X)center on the electron-to-hole mass ratio for a few values of the distance d between the fixed negative ion on the z axis and the dot plane is obtained.We find that when d → 0,the barrier (A-,X) center has not any bound state.We also studied the stability and binding energy of the ground state of the barrier (A-,X) center in a parabolic quantum dot as a function of the distance d between the fixed negative ion on the z axis and the dot plane.``

  18. Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase.

    Directory of Open Access Journals (Sweden)

    Daniel R Ripoll

    Full Text Available Quantitatively predicting changes in drug sensitivity associated with residue mutations is a major challenge in structural biology. By expanding the limits of free energy calculations, we successfully identified mutations in influenza neuraminidase (NA that confer drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD with Hamiltonian Replica Exchange and calculated binding free energy changes for H274Y, N294S, and Y252H mutants. Based on experimental data, our calculations achieved high accuracy and precision compared with results from established computational methods. Analysis of 15 micros of aggregated MD trajectories provided insights into the molecular mechanisms underlying drug resistance that are at odds with current interpretations of the crystallographic data. Contrary to the notion that resistance is caused by mutant-induced changes in hydrophobicity of the binding pocket, our simulations showed that drug resistance mutations in NA led to subtle rearrangements in the protein structure and its dynamics that together alter the active-site electrostatic environment and modulate inhibitor binding. Importantly, different mutations confer resistance through different conformational changes, suggesting that a generalized mechanism for NA drug resistance is unlikely.

  19. Hyperon binding energy in Λ6He and Λ7He

    Directory of Open Access Journals (Sweden)

    Filikhin Igor

    2016-01-01

    Full Text Available The three-body approach based on the configuration space Faddeev equations for systems of non-identical particles is proposed to describe light hypernuclei (A=6,7, S=-1 with α particle clustering. We focus on the model (α +Λ + n + n for Λ7He hypernucleus for which the first experimental data have been recently reported. New evaluation for hyperon binding energy in Λ7He is done by using a relation between energies of the spin doublet (1−,2− of Λ6He and the Λ7He ground state. Energies of low-lying levels of Λ6He hypernucleus are calculated within the cluster α + Λ + n model.

  20. Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA.

    Science.gov (United States)

    Xiao, Xingqing; Hung, Michelle E; Leonard, Joshua N; Hall, Carol K

    2016-10-15

    Our previously developed peptide-design algorithm was improved by adding an energy minimization strategy which allows the amino acid sidechains to move in a broad configuration space during sequence evolution. In this work, the new algorithm was used to generate a library of 21-mer peptides which could substitute for λ N peptide in binding to boxB RNA. Six potential peptides were obtained from the algorithm, all of which exhibited good binding capability with boxB RNA. Atomistic molecular dynamics simulations were then conducted to examine the ability of the λ N peptide and three best evolved peptides, viz. Pept01, Pept26, and Pept28, to bind to boxB RNA. Simulation results demonstrated that our evolved peptides are better at binding to boxB RNA than the λ N peptide. Sequence searches using the old (without energy minimization strategy) and new (with energy minimization strategy) algorithms confirm that the new algorithm is more effective at finding good RNA-binding peptides than the old algorithm. © 2016 Wiley Periodicals, Inc.

  1. AIScore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes.

    Science.gov (United States)

    Raub, Stephan; Steffen, Andreas; Kämper, Andreas; Marian, Christel M

    2008-07-01

    In this work we report on a novel scoring function that is based on the LUDI model and focuses on the prediction of binding affinities. AIScore extends the original FlexX scoring function using a chemically diverse set of hydrogen-bonded interactions derived from extensive quantum chemical ab initio calculations. Furthermore, we introduce an algorithmic extension for the treatment of multifurcated hydrogen bonds (XFurcate). Charged and resonance-assisted hydrogen bond energies and hydrophobic interactions as well as a scaling factor for implicit solvation were fitted to experimental data. To this end, we assembled a set of 101 protein-ligand complexes with known experimental binding affinities. Tightly bound water molecules in the active site were considered to be an integral part of the binding pocket. Compared to the original FlexX scoring function, AIScore significantly improves the prediction of the binding free energies of the complexes in their native crystal structures. In combination with XFurcate, AIScore yields a Pearson correlation coefficient of R P = 0.87 on the training set. In a validation run on the PDBbind test set we achieved an R P value of 0.46 for 799 attractively scored complexes, compared to a value of R P = 0.17 and 739 bound complexes obtained with the FlexX original scoring function. The redocking capability of AIScore, on the other hand, does not fully reach the good performance of the original FlexX scoring function. This finding suggests that AIScore should rather be used for postscoring in combination with the standard FlexX incremental ligand construction scheme.

  2. Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel

    2014-07-03

    Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is

  3. Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation.

    Science.gov (United States)

    Tsujikawa, Hiroto; Sato, Kenta; Wei, Cao; Saad, Gul; Sumikoshi, Kazuya; Nakamura, Shugo; Terada, Tohru; Shimizu, Kentaro

    2016-09-01

    We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction.

  4. Anisotropic Lithium Insertion Behavior in Silicon Nanowires: Binding Energy, Diffusion Barrier, and Strain Effect

    KAUST Repository

    Zhang, Qianfan

    2011-05-19

    Silicon nanowires (SiNWs) have recently been shown to be promising as high capacity lithium battery anodes. SiNWs can be grown with their long axis along several different crystallographic directions. Due to distinct atomic configuration and electronic structure of SiNWs with different axial orientations, their lithium insertion behavior could be different. This paper focuses on the characteristics of single Li defects, including binding energy, diffusion barriers, and dependence on uniaxial strain in [110], [100], [111], and [112] SiNWs. Our systematic ab initio study suggests that the Si-Li interaction is weaker when the Si-Li bond direction is aligned close to the SiNW long axis. This results in the [110] and [111] SiNWs having the highest and lowest Li binding energy, respectively, and it makes the diffusion barrier along the SiNW axis lower than other pathways. Under external strain, it was found that [110] and [001] SiNWs are the most and least sensitive, respectively. For diffusion along the axial direction, the barrier increases (decreases) under tension (compression). This feature results in a considerable difference in the magnitude of the energy barrier along different diffusion pathways. © 2011 American Chemical Society.

  5. Binding Energies of Excitons in Square Quantum-Well Wires in the Presence of a Magnetic Field

    Institute of Scientific and Technical Information of China (English)

    张迎涛; 邸冰; 谢尊; 李有成

    2004-01-01

    The binding energies of the ground state of excitons in the GaAs/Ga1-xAlxAs square quantum-well wire in the presence of a magnetic field are investigated by using the variational method. It is assumed that the magnetic field is applied parallel to the axis of the wire. The calculations of the binding energy as a function of the wire size have been performed for infinite and finite confinement potentials. The contribution of the magnetic field makes the binding energy larger obviously, particularly for the wide wire, and the magnetic field is much more pronounced for the binding energy in a square quantum wire than that in a cylindrical quantum wire. The mismatch of effective masses between the well and the barrier is also considered in the calculation.

  6. Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane

    Science.gov (United States)

    Vivcharuk, Victor; Tomberli, Bruno; Tolokh, Igor S.; Gray, C. G.

    2008-03-01

    Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05±0.39kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.

  7. Addendum: Triton and hypertriton binding energies calculated from SU_6 quark-model baryon-baryon interactions

    CERN Document Server

    Fujiwara, Y; Kohno, M; Miyagawa, K

    2007-01-01

    Previously we calculated the binding energies of the triton and hypertriton, using an SU_6 quark-model interaction derived from a resonating-group method of two baryon clusters. In contrast to the previous calculations employing the energy-dependent interaction kernel, we present new results using a renormalized interaction, which is now energy independent and reserves all the two-baryon data. The new binding energies are slightly smaller than the previous values. In particular the triton binding energy turns out to be 8.14 MeV with a charge-dependence correction of the two-nucleon force, 190 keV, being included. This indicates that about 350 keV is left for the energy which is to be accounted for by three-body forces.

  8. Fabrication of CuCl quantum dots and the size dependence of the biexciton binding energy

    CERN Document Server

    Park, S T; Kim, H Y; Kim, I G

    2000-01-01

    We fabricated CuCl quantum dots (QDs) in an aluminoborosilicate glass matrix. The photoluminescence of the CuCl QDs was surveyed by using the band-to-band excitation and the site selective luminescence methods. The excitation density dependence of the exciton and the biexciton luminescence was measured, and the saturation effects of the luminescence intensities were observed. The biexciton binding energies measured using the site selective luminescence method increased with decreasing QD size. The data were well fitted by a function resulting from the numerical matrix-diagonalization method.

  9. Evolution of Structure in Nuclei: Meditation by Sub-Shell Modifications and Relation to Binding Energies

    Science.gov (United States)

    Casten, R. F.; Cakirli, R. B.

    2009-03-01

    Understanding the development of configuration mixing, coherence, collectivity, and deformation in nuclei is one of the crucial challenges in nuclear structure physics, and one which has become all the more important with the advent of next generation facilities for the study of exotic nuclei. We will discuss recent work on phase/shape transitional behavior in nuclei, and the role of changes in sub-shell structure in mediating such transitional regions. We will also discuss a newly found, much deeper, link between nuclear structure and nuclear binding energies.

  10. Transition between quasi 2 and 3D behaviour of the binding energy of screened excitons in semiconductor quantum well structures

    CERN Document Server

    Vazquez, G J; Reyes, J A; Lee, J; Spector, H N

    2003-01-01

    We have calculated the binding energy of screened excitons in a semiconducting quantum well structure as a function of screening parameter and the width of the quantum well using variational wave functions to obtain upper bounds for the energy. The binding energy decreases with increasing values of the screening parameter and with increasing well width. However, as long as the well width is narrow enough so the electrons and holes occupy their lowest-energy subbands, the exciton remains bound even for large values of the screening parameter whenever the electron gas remains nondegenerate. (Author)

  11. The formation mechanism and the binding energy of the body-centred regular tetrahedral structure of He+5

    Institute of Scientific and Technical Information of China (English)

    李萍; 熊勇; 芶清泉; 张建平

    2002-01-01

    We propose the formation mechanism of the body-centred regular tetrahedral structure of the He+5 cluster. The total energy curve for this structure has been calculated by using a modified arrangement channel quantum mechanics method. The result shows that a minimal energy of -13.9106 a.u. occurs at a separation of 1.14a0 between the nucleus at the centre and nuclei at the apexes. Therefore we obtain the binding energy of 0.5202 a.u. for this structure. This means that the He+5 cluster may be stable with a high binding energy in a body-centred regular tetrahedral structure.

  12. On the Binding Energy and the Charge Symmetry Breaking in A<=16 Lambda-hypernuclei

    CERN Document Server

    Botta, E; Feliciello, A

    2016-01-01

    Recent achievements in hypernuclear spectroscopy, in particular the determination of the $\\Lambda$-binding energy B$_{\\Lambda}$ by high precision magnetic spectrometry, contributed to stimulate considerably the search for Charge Symmetry Breaking effects in $\\Lambda$-hypernuclei isomultiplets. We have reorganized the results from the FINUDA experiment and we have produced a list of B$_{\\Lambda}$ values for hypernuclei with A$\\leq$16 considering only the data from magnetic spectrometers with an absolute calibration of the energy scale (FINUDA at DA$\\Phi$NE and electroproduction experiments). By comparing them with the corresponding B$_{\\Lambda}$ from the emulsion experiments, we observe that there is a systematic small difference that is taken into account. A synopsis of all the results on B$_{\\Lambda}$ so far published is finally suggested. Several interesting conclusions are drawn, among which the equality within the errors of B$_{\\Lambda}$ for the A=7, 12, 16 isomultiplets, based only on recent spectrometri...

  13. Pion tensor force and nuclear binding energy in the relativistic Hartree-Fock formalism

    Science.gov (United States)

    Marcos, S.; López-Quelle, M.; Niembro, R.; Savushkin, L. N.

    2014-03-01

    The binding energies of several isotopic families are studied within the relativistic Hartree-Fock approximation with the pseudovector coupling for the πN vertex, to find out a suitable strength for the effective pion tensor force (EPTF). An approximation for determining separately the contributions of the central and tensor forces generated by pion is considered. The results for heavy nuclei indicate that a realistic strength for the EPTF is smaller than a half of that appearing in the OPEP. This conclusion also applies to the results for the single-particle energies. Besides, it has been found that there is a genuine relativistic contribution of the EPTF in nuclear matter which is small but significant.

  14. Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method.

    Science.gov (United States)

    Ngo, Son Tung; Mai, Binh Khanh; Hiep, Dinh Minh; Li, Mai Suan

    2015-10-01

    The binding mechanism of AC1NX476 to HIV-1 protease wild type and mutations was studied by the docking and molecular dynamics simulations. The binding free energy was calculated using the double-annihilation binding free energy method. It is shown that the binding affinity of AC1NX476 to wild type is higher than not only ritonavir but also darunavir, making AC1NX476 become attractive candidate for HIV treatment. Our theoretical results are in excellent agreement with the experimental data as the correlation coefficient between calculated and experimentally measured binding free energies R = 0.993. Residues Asp25-A, Asp29-A, Asp30-A, Ile47-A, Gly48-A, and Val50-A from chain A, and Asp25-B from chain B play a crucial role in the ligand binding. The mutations were found to reduce the receptor-ligand interaction by widening the binding cavity, and the binding propensity is mainly driven by the van der Waals interaction. Our finding may be useful for designing potential drugs to combat with HIV.

  15. Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent:  Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase.

    Science.gov (United States)

    Su, Yang; Gallicchio, Emilio; Das, Kalyan; Arnold, Eddy; Levy, Ronald M

    2007-01-01

    Expressions for Linear Interaction Energy (LIE) estimators for the binding of ligands to a protein receptor in implicit solvent are derived based on linear response theory and the cumulant expansion expression for the free energy. Using physical arguments, values of the LIE linear response proportionality coefficients are predicted for the explicit and implicit solvent electrostatic and van der Waals terms. Motivated by the fact that the receptor and solution media may respond differently to the introduction of the ligand, a novel form of the LIE regression equation is proposed to model independently the processes of insertion of the ligand in the receptor and in solution. We apply these models to the problem of estimating the binding free energy of two non-nucleoside classes of inhibitors of HIV-1 RT (HEPT and TIBO analogues). We develop novel regression models with greater predictive ability than more standard LIE formulations. The values of the regression coefficients generally conform to linear response predictions, and we use this fact to develop a LIE regression equation with only one adjustable parameter (excluding the intercept parameter) which is superior to the other models we tested and to previous results in terms of predictive accuracy for the HEPT and TIBO compounds individually. The new models indicate that, due to the different effects of induced steric strain of the receptor, an increase of ligand size alone opposes binding for ligands of the HEPT class, whereas it favors binding for ligands of the TIBO class.

  16. Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP.

    Science.gov (United States)

    Bayden, Alexander S; Moustakas, Demetri T; Joseph-McCarthy, Diane; Lamb, Michelle L

    2015-08-24

    The SZMAP method computes binding free energies and the corresponding thermodynamic components for water molecules in the binding site of a protein structure [ SZMAP, 1.0.0 ; OpenEye Scientific Software Inc. : Santa Fe, NM, USA , 2011 ]. In this work, the ability of SZMAP to predict water structure and thermodynamic stability is examined for the X-ray crystal structures of a series of protein-ligand complexes. SZMAP results correlate with higher-level replica exchange thermodynamic integration double decoupling calculations of the absolute free energy of bound waters in the test set complexes. In addition, SZMAP calculations show good agreement with experimental data in terms of water conservation (across multiple crystal structures) and B-factors over a subset of the test set. In particular, the SZMAP neutral entropy difference term calculated at crystallographic water positions within each of the complex structures correlates well with whether that crystallographic water is conserved or displaceable. Furthermore, the calculated entropy of the water probe relative to the continuum shows a significant degree of correlation with the B-factors associated with the oxygen atoms of the water molecules. Taken together, these results indicate that SZMAP is capable of quantitatively predicting water positions and their energetics and is potentially a useful tool for determining which waters to attempt to displace, maintain, or build in through water-mediated interactions when evolving a lead series during a drug discovery program.

  17. Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.

    Directory of Open Access Journals (Sweden)

    Rafael Tapia-Rojo

    2014-10-01

    Full Text Available The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes. We use a computational method to analyze promoters from a given genome. Our approach is based on a physical model at the mesoscopic level of protein-DNA interaction based on the influence of DNA local conformation on the dynamics of a general particle along the chain. Following the proposed model, the joined dynamics of the protein particle and the DNA portion of interest, only characterized by its base pair sequence, is simulated. The simulation output is analyzed by generating and analyzing the Free Energy Landscape of the system. In order to prove the capacity of prediction of our computational method we have analyzed nine promoters of Anabaena PCC 7120. We are able to identify the transcription starting site of each of the promoters as the most populated macrostate in the dynamics. The developed procedure allows also to characterize promoter macrostates in terms of thermo-statistical magnitudes (free energy and entropy, with valuable biological implications. Our results agree with independent previous experimental results. Thus, our methods appear as a powerful complementary tool for identifying protein binding sites in promoter sequences.

  18. Chaperone driven polymer translocation through Nanopore: spatial distribution and binding energy

    CERN Document Server

    Abdolvahab, Rouhollah Haji

    2016-01-01

    Chaperones are binding proteins which work as a driving force to bias the biopolymer translocation by binding to it near the pore and preventing its backsliding. Chaperones may have different spatial distribution. Recently we show the importance of their spatial distribution in translocation and how it effects on sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. As a result of the exponential distribution of chaperones, energy dependency of the translocation time will changed and one see a minimum in translocation time versus effective energy curve. The same trend can be seen in scaling exponent of time versus polymer length, $\\beta$ ($T\\sim\\beta$). Interestingly in some special cases e.g. chaperones of size $\\lambda=6$ and with exponential distribution rate of $\\alpha=5$, the minimum reaches even to amount of less than $1$ ($\\beta<1$). We explain the possibility of this rare result and base on a theoretical discussion we show that by taking into acc...

  19. Effect of magnetic field on the impurity binding energy of the excited states in spherical quantum dot

    Indian Academy of Sciences (India)

    E Sadeghi; Gh Rezaie

    2010-10-01

    The effect of external magnetic field on the excited state energies in a spherical quantum dot was studied. The impurity energy and binding energy were calculated using the variational method within the effective mass approximation and finite barrier potential. The results showed that by increasing the magnetic field, the energy would be increased. The results obtained by this method were compared with the previous investigations.

  20. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies.

    Science.gov (United States)

    Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

    2011-06-02

    The independent trajectory thermodynamic integration (IT-TI) approach (Lawrenz et. al J. Chem. Theory. Comput. 2009, 5:1106-1116(1)) for free energy calculations with distributed computing is employed to study two distinct cases of protein-ligand binding: first, the influenza surface protein N1 neuraminidase bound to the inhibitor oseltamivir, and second, the M. tuberculosis enzyme RmlC complexed with the molecule CID 77074. For both systems, finite molecular dynamics (MD) sampling and varied molecular flexibility give rise to IT-TI free energy distributions that are remarkably centered on the target experimental values, with a spread directly related to protein, ligand, and solvent dynamics. Using over 2 μs of total MD simulation, alternative protocols for the practical, general implementation of IT-TI are investigated, including the optimal use of distributed computing, the total number of alchemical intermediates, and the procedure to perturb electrostatics and van der Waals interactions. A protocol that maximizes predictive power and computational efficiency is proposed. IT-TI outperforms traditional TI predictions and allows a straightforward evaluation of the reliability of free energy estimates. Our study has broad implications for the use of distributed computing in free energy calculations of macromolecular systems.

  1. Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

    Science.gov (United States)

    Duan, Lili; Liu, Xiao; Zhang, John Z H

    2016-05-04

    Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

  2. Quantum mechanical treatment of binding energy between DNA nucleobases and carbon nanotube: A DFT analysis

    Science.gov (United States)

    Chehel Amirani, Morteza; Tang, Tian; Cuervo, Javier

    2013-12-01

    The interactions between DNA and carbon nanotubes (CNTs) have been widely studied in recent years. The binding process of DNA with CNT as well as the electronic properties of DNA/CNT hybrids constitutes an interesting yet complicated problem. The binding energy (BE) of the hybridization is one of the most extensively studied parameters for the problem. In this work, density functional theory (DFT) was used to perform geometry optimization of neutral nucleobases including adenine, cytosine, guanine and thymine absorbed on a zigzag (7,0) single-walled CNT and to evaluate the basis set superposition error corrected BE of the optimized configuration. All DFT calculations were performed using the M05-2X functional. The 6-31G(d) basis set was used for the optimization step and single point energy calculations were done using the 6-31G(d,p) basis set. For each nucleobase, we examined the influence of the initial configuration (IC) on the BE value. In particular, we considered 24 different ICs for each nucleobase, and each IC was subjected to an independent optimization and BE calculation. Our results showed that different ICs result in very different BE values and can even change the order of the BE corresponding to different nucleobases. The difference in the BE for a particular nucleobase caused by changes in its IC can be comparable to the difference in the BE between different nucleobases at the same initial position relative to the CNT. This provides an explanation for the discrepancies that exist in the literature on the nucleobase/CNT BE, and suggests that the potential energy surface between the nucleobases and the CNT can have many local minima and care should be exercised in the calculation and interpretation of the BE.

  3. Binding Energy and Lifetime of Excitons in InxGa1-xAs/GaAs Quantum Wells

    DEFF Research Database (Denmark)

    Orani, D.; Polimeni, A.; Patane, A.;

    1997-01-01

    We report a systematic study of exciton binding energies and lifetimes in InGaAs/GaAs quantum wells. The experimental binding energies have been deduced from photoluminescence excitation measurements taking into account the contribution of the 2s state of the exciton and the line broadening....... The experimental results have been compared with accurate calculations in a four-band model, where exciton energies take into account the polaron correction. The theory accounts for all the experimental observations and provides a good quantitative agreement with the experimental values....

  4. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.

    Science.gov (United States)

    Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

    2012-01-01

    The Independent-Trajectory Thermodynamic Integration (IT-TI) approach for free energy calculation with distributed computing is described. IT-TI utilizes diverse conformational sampling obtained from multiple, independent simulations to obtain more reliable free energy estimates compared to single TI predictions. The latter may significantly under- or over-estimate the binding free energy due to finite sampling. We exemplify the advantages of the IT-TI approach using two distinct cases of protein-ligand binding. In both cases, IT-TI yields distributions of absolute binding free energy estimates that are remarkably centered on the target experimental values. Alternative protocols for the practical and general application of IT-TI calculations are investigated. We highlight a protocol that maximizes predictive power and computational efficiency.

  5. Improving the Volume Dependence of Two-Body Binding Energies Calculated with Lattice QCD

    CERN Document Server

    Davoudi, Zohreh

    2011-01-01

    Volume modifications to the binding of two-body systems in large cubic volumes of extent L depend upon the total momentum and exponentially upon the ratio of L to the size of the boosted system. Recent work by Bour et al determined the momentum dependence of the leading volume modifications to nonrelativistic systems with periodic boundary conditions imposed on the single-particle wavefunctions, enabling them to numerically determine the scattering of such bound states using a low-energy effective field theory and Luschers finite-volume method. The calculation of bound nuclear systems directly from QCD using Lattice QCD has begun, and it is important to reduce the systematic uncertainty introduced into such calculations by the finite spatial extent of the gauge-field configurations. We extend the work of Bour et al from nonrelativistic quantum mechanics to quantum field theory by generalizing the work of Luscher and of Gottlieb and Rummukainen to boosted two-body bound states. The volume modifications to bind...

  6. Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis.

    Science.gov (United States)

    Morozenko, A; Leontyev, I V; Stuchebrukhov, A A

    2014-10-14

    The energetics of water molecules in proteins is studied using the water placement software Dowser. We compared the water position predictions for 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules. From the analysis of the outputs of Dowser with variable parameters and comparison with experimental X-ray data, we derived an estimate of the average dipole moment of water molecules located in the internal cavities of the protein and their binding energies. The water parameters thus obtained from the experimental data are then analyzed within the framework of charge-scaling theory developed recently by this group; the parameters are shown to be in good agreement with the predictions that the theory makes for the dipole moment in a protein environment. The water dipole in the protein environment is found to be much different from that in the bulk and in such models as SPC or TIPnP. The role of charge scaling due to electronic polarizability of the protein is discussed.

  7. On the binding energy and the charge symmetry breaking in A ≤ 16 Λ-hypernuclei

    Science.gov (United States)

    Botta, E.; Bressani, T.; Feliciello, A.

    2017-04-01

    In recent years, several experiments using magnetic spectrometers provided high precision results in the field of Hypernuclear Physics. In particular, the accurate determination of the Λ-binding energy, BΛ, contributed to stimulate considerably the discussion about the Charge Symmetry Breaking effect in Λ-hypernuclei isomultiplets. We have reorganized the results from the FINUDA experiment and we have obtained a series of BΛ values for Λ-hypernuclei with A≤ 16 by taking into account data only from magnetic spectrometers implementing an absolute calibration of the energy scale (FINUDA at DAΦNE and electroproduction experiments at JLab and at MaMi). We have then critically revisited the results obtained at KEK by the SKS Collaboration in order to make possible a direct comparison between data from experiments with and without such an absolute energy scale. A synopsis of recent spectrometric measurements of BΛ is presented, including also emulsion experiment results. Several interesting conclusions are drawn, among which the equality within the errors of BΛ for the A = 7 , 12 , 16 isomultiplets, based only on recent spectrometric data. This observation is in nice agreement with a recent theoretical prediction. Ideas for possible new measurements which should improve the present experimental knowledge are finally put forward.

  8. Reveal of small alkanes and isomers using calculated core and valence binding energy spectra and total momentum cross sections

    CERN Document Server

    Yang, Zejin

    2013-01-01

    The present study revealed quantum mechanically that the C1s binding energy spectra of the small alkanes (upto six carbons) provide a clear picture of isomeric chemical shift in linear alkanes and branched isomers, whereas the valence binding energy spectra contain more sensitive information regarding the length of the carbon chains. Total momentum cross sections of the alkanes exhibit the information of the chain length as well as constitutional isomers of the small alkanes. The C1s binding energies of small alkanes (including isomers) are position specific and the terminal carbons have the lowest energies. The length of an alkane chain does not apparently affect the C1s energies so that the terminal carbons (289.11 eV) of pentane are almost the same as those of hexane. The valence binding energy spectra of the alkanes are characterized by inner valence and outer valence regions which are separated by an energy gap at approximately 17 eV. The intensities of the total momentum cross sections of the alkanes ar...

  9. Role of Codeposited Impurities in Growth: Dependence of Morphology on Binding and Barrier Energies

    Science.gov (United States)

    Sathiyanarayanan, Rajesh; Hamouda, A. Bh.; Pimpinelli, A.; Einstein, T. L.

    2010-03-01

    The previous talk showed that codeposition of impurity atoms during epitaxial growth could be used for nanostructuring of surfaces. Based on their lateral nearest-neighbor binding energies (ENN) to Cu and their diffusion barriers (Ed) on Cu(001), we classify the candidate impurity atoms into four sets. We find that codeposition of impurities from different sets produce qualitatively different surface morphologies both in the step-flow and the submonolayer (θ<= 0.7 ML) regimes. In the submonolayer regime, we characterize these differences through variations of the number of islands (Ni) and the average island size with coverage (θ). Further, we compute the critical nucleus size (i) for all of these cases from the distribution of capture-zone areas using the generalized Wigner distribution.footnotetextA. Pimpinelli, T. L. Einstein, Phys. Rev. Lett. 99, 226102 (2007).

  10. Spin assignments of nuclear levels above the neutron binding energy in $^{88}$Sr

    CERN Multimedia

    Neutron resonances reveal nuclear levels in the highly excited region of the nucleus around the neutron binding energy. Nuclear level density models are therefore usually calibrated to the number of observed levels in neutron-induced reactions. The gamma-ray cascade from the decay of the highly excited compound nucleus state to the ground state show dierences dependent on the initial spin. This results in a dierence in the multiplicity distribution which can be exploited. We propose to use the 4${\\pi}$ total absorption calorimeter (TAC) at the n TOF facility to determine the spins of resonances formed by neutrons incident on a metallic $^{87}$Sr sample by measuring the gamma multiplicity distributions for the resolved resonances. In addition we would like to use the available enriched $^{87}$Sr target for cross section measurements with the C$\\scriptscriptstyle{6}$D$\\scriptscriptstyle{6}$ detector setup.

  11. Exciton binding energies and absorption in intermixed GaAs-AlGaAs quantum wells

    Science.gov (United States)

    Meney, Alistair T.

    1992-12-01

    The optical properties of excitons in layer-intermixed GaAs-AlGaAs quantum wells are studied theoretically. The electronic dispersion is obtained using the 6×6 Luttinger-Kohn Hamiltonian for the valence bands, and an accurate expression for the conduction band dispersion which includes the effects of nonparabolicity and warping to fourth order in k. The HH1-CB1 (1s) and LH1-CB1(1s) exciton binding energies are calculated as a function of diffusion time. The absorption for both TE and TM polarization is obtained at several wavelengths, and is seen to decrease significantly with increased intermixing. The decrease in absorption is larger for narrow wells, where the effects of intermixing are more pronounced for a given diffusion time.

  12. Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

    KAUST Repository

    Beke-Somfai, Tamás

    2010-01-26

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

  13. Benchmarking ab initio binding energies of hydrogen-bonded molecular clusters based on FTIR spectroscopy

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Du, Lin; Reiman, Heidi;

    2014-01-01

    Models of formation and growth of atmospheric aerosols are highly dependent on accurate cluster binding energies. These are most often calculated by ab initio electronic structure methods but remain associated with significant uncertainties. We present a computational benchmarking study......) and compare this range to predictions from several widely used electronic structure methods, including five density functionals, Møller-Plesset perturbation theory, and five coupled cluster methods up to CCSDT quality, considering also the D3 dispersion correctional scheme. With some exceptions, we find...... that most electronic structure methods overestimate ΔG°295 K. The effects of vibrational anharmonicity is approximated using scaling factors, reducing ΔG°295 K by ca. 1.8 kJ mol(-1), whereby ΔG°295 K predictions well within the experimental range can be obtained....

  14. Potential energy surface and binding energy in the presence of an external electric field: modulation of anion-π interactions for graphene-based receptors.

    Science.gov (United States)

    Foroutan-Nejad, Cina; Marek, Radek

    2014-02-14

    Measuring the binding energy or scanning the potential energy surface (PES) of the charged molecular systems in the presence of an external electric field (EEF) requires a careful evaluation of the origin-dependency of the energy of the system and references. Scanning the PES for charged or purely ionic systems for obtaining the intrinsic energy barriers needs careful analysis of the electric work applied on ions by the EEF. The binding energy in the presence of an EEF is different from that in the absence of an electric field as the binding energy is an anisotropic characteristic which depends on the orientation of molecules with respect to the EEF. In this contribution we discuss various aspects of the PES and the concept of binding energy in the presence of an EEF. In addition, we demonstrate that the anion-π bonding properties can be modulated by applying a uniform EEF, which has a more pronounced effect on the larger, more polarizable π-systems. An analogous behavior is presumed for cation-π systems. We predict that understanding the phenomenon introduced in the present account has enormous potential, for example, for separating charged species on the surface of polarizable two-dimensional materials such as graphene or the surface of carbon nanotubes, in desalination of water.

  15. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.

    Science.gov (United States)

    Reif, Maria M; Oostenbrink, Chris

    2014-01-30

    The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.

  16. Optimizing the Binding Energy of Hydrogen on Nanostructured Carbon Materials through Structure Control and Chemical Doping

    Energy Technology Data Exchange (ETDEWEB)

    Jie Liu

    2011-02-01

    The DOE Hydrogen Sorption Center of Excellence (HSCoE) was formed in 2005 to develop materials for hydrogen storage systems to be used in light-duty vehicles. The HSCoE and two related centers of excellence were created as follow-on activities to the DOE Office of Energy Efficiency and Renewable Energy’s (EERE’s) Hydrogen Storage Grand Challenge Solicitation issued in FY 2003. The Hydrogen Sorption Center of Excellence (HSCoE) focuses on developing high-capacity sorbents with the goal to operate at temperatures and pressures approaching ambient and be efficiently and quickly charged in the tank with minimal energy requirements and penalties to the hydrogen fuel infrastructure. The work was directed at overcoming barriers to achieving DOE system goals and identifying pathways to meet the hydrogen storage system targets. To ensure that the development activities were performed as efficiently as possible, the HSCoE formed complementary, focused development clusters based on the following four sorption-based hydrogen storage mechanisms: 1. Physisorption on high specific surface area and nominally single element materials 2. Enhanced H2 binding in Substituted/heterogeneous materials 3. Strong and/or multiple H2 binding from coordinated but electronically unsatruated metal centers 4. Weak Chemisorption/Spillover. As a member of the team, our group at Duke studied the synthesis of various carbon-based materials, including carbon nanotubes and microporous carbon materials with controlled porosity. We worked closely with other team members to study the effect of pore size on the binding energy of hydrogen to the carbon –based materials. Our initial project focus was on the synthesis and purification of small diameter, single-walled carbon nanotubes (SWNTs) with well-controlled diameters for the study of their hydrogen storage properties as a function of diameters. We developed a chemical vapor deposition method that synthesized gram quantities of carbon nanotubes with

  17. Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

    Directory of Open Access Journals (Sweden)

    Caselle Michele

    2007-09-01

    Full Text Available Abstract Background Specific binding of proteins to DNA is one of the most common ways gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a simple recognition code, therefore the prediction of DNA target sequences is not straightforward. DNA-protein interactions can be studied using computational methods which can complement the current experimental methods and offer some advantages. In the present work we use physical effective potentials to evaluate the DNA-protein binding affinities for the λ repressor-DNA complex for which structural and thermodynamic experimental data are available. Results The binding free energy of two molecules can be expressed as the sum of an intermolecular energy (evaluated using a molecular mechanics forcefield, a solvation free energy term and an entropic term. Different solvation models are used including distance dependent dielectric constants, solvent accessible surface tension models and the Generalized Born model. The effect of conformational sampling by Molecular Dynamics simulations on the computed binding energy is assessed; results show that this effect is in general negative and the reproducibility of the experimental values decreases with the increase of simulation time considered. The free energy of binding for non-specific complexes, estimated using the best energetic model, agrees with earlier theoretical suggestions. As a results of these analyses, we propose a protocol for the prediction of DNA-binding target sequences. The possibility of searching regulatory elements within the bacteriophage λ genome using this protocol is explored. Our analysis shows good prediction capabilities, even in absence of any thermodynamic data and information on the naturally recognized sequence. Conclusion This study supports the conclusion that physics-based methods can offer a completely complementary

  18. Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Olsen, Lars; Jørgensen, Flemming Steen;

    2010-01-01

    , and methods based on statistical mechanics. In the present investigation, we started from an LIE model to predict the binding free energy of structurally diverse compounds of cytochrome P450 1A2 ligands, one of the important human metabolizing isoforms of the cytochrome P450 family. The data set includes both...... substrates and inhibitors. It appears that the electrostatic contribution to the binding free energy becomes negligible in this particular protein and a simple empirical model was derived, based on a training set of eight compounds. The root mean square error for the training set was 3.7 kJ/mol. Subsequent......Predicting binding affinities for receptor-ligand complexes is still one of the challenging processes in computational structure-based ligand design. Many computational methods have been developed to achieve this goal, such as docking and scoring methods, the linear interaction energy (LIE) method...

  19. Experimentally Determined Binding Energies of Astrophysically Relevant Hydrocarbons in Pure and H2O-Layered Ices

    Science.gov (United States)

    Behmard, Aida; Graninger, Dawn; Fayolle, Edith; Oberg, Karin I.

    2017-01-01

    Small hydrocarbons represent an important organic reservoir in a variety of interstellar environments. Constraints on desorption temperatures and binding energies of hydrocarbons are thus necessary for accurate predictions of where and in which phase these molecules exist. Through a series of temperature programmed desorption experiments, we determined binding energies of 1, 2, and 3-carbon interstellar hydrocarbons (CH4, C2H2, C2H4, C2H6, C3H4, C3H6, and C3H8) in pure ices and in relation to water ice, the dominant ice constituent during star and planet formation. These empirically determined values can be used to inform observations and models of the molecular spatial distribution in protoplanetary disks, thus providing insight into planetesimal composition. In addition, knowledge of hydrocarbon binding energies will refine simulations of grain surface chemistry, allowing for better predictions of the chemical conditions that lead to the production of complex organic molecules vital for life.

  20. Exciton and donor binding energies in quantum-well wires and quantum dots a fractional-dimensional space approach

    Institute of Scientific and Technical Information of China (English)

    Li Hong; Kong Xiao-Jun

    2004-01-01

    A simple method for calculating the free-exciton binding energies in the fractional-dimensional-space model for single-quantum-well structure has been extended to quantum-well wires and quantum dots, in which the real anisotropic system is modelled through an effective isotropic environment with a fractional dimension. In this scheme, the fractionaldimensional parameter is chosen via an analytical procedure and involves no ansatz. We calculated the ground-state binding energies of excitons and donors in quantum-well wires with rectangular cross sections. Our results are found to be in good agreement with previous variational calculations and available experimental measurements. We also discussed the ground-state exciton binding energy changing with different shapes of quantum-well wires.

  1. Binding energies of trions and biexcitons in two-dimensional semiconductors from diffusion quantum Monte Carlo calculations

    Science.gov (United States)

    Szyniszewski, M.; Mostaani, E.; Drummond, N. D.; Fal'ko, V. I.

    2017-02-01

    Excitonic effects play a particularly important role in the optoelectronic behavior of two-dimensional (2D) semiconductors. To facilitate the interpretation of experimental photoabsorption and photoluminescence spectra we provide statistically exact diffusion quantum Monte Carlo binding-energy data for Mott-Wannier models of excitons, trions, and biexcitons in 2D semiconductors. We also provide contact pair densities to allow a description of contact (exchange) interactions between charge carriers using first-order perturbation theory. Our data indicate that the binding energy of a trion is generally larger than that of a biexciton in 2D semiconductors. We provide interpolation formulas giving the binding energy and contact density of 2D semiconductors as functions of the electron and hole effective masses and the in-plane polarizability.

  2. Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.

    Directory of Open Access Journals (Sweden)

    Adrien Nicolaï

    Full Text Available ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD of Hsp70 propagates a signal to its substrate-binding domain (SBD. Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in

  3. Role of codeposited impurities during growth. II. Dependence of morphology on binding and barrier energies

    Science.gov (United States)

    Sathiyanarayanan, Rajesh; Hamouda, Ajmi Bh.; Pimpinelli, A.; Einstein, T. L.

    2011-01-01

    In an accompanying article we showed that surface morphologies obtained through codeposition of a small quantity (2%) of impurities with Cu during growth (step-flow mode, θ = 40 ML) significantly depends on the lateral nearest-neighbor binding energy (ENN) to Cu adatom and the diffusion barrier (Ed) of the impurity atom on Cu(0 0 1). Based on these two energy parameters, ENN and Ed, we classify impurity atoms into four sets. We study island nucleation and growth in the presence of codeposited impurities from different sets in the submonolayer (θ⩽ 0.7 ML) regime. Similar to growth in the step-flow mode, we find different nucleation and growth behavior for impurities from different sets. We characterize these differences through variations of the number of islands (Ni) and the average island size with coverage (θ). Further, we compute the critical nucleus size (i) for all of these cases from the distribution of capture-zone areas using the generalized Wigner distribution.

  4. Binding energies of the lithium isoelectronic sequence approaching the critical charge

    Science.gov (United States)

    Katriel, Jacob; Puchalski, Mariusz; Pachucki, Krzysztof

    2012-10-01

    The Simon-Zhislin-Hunziker theorem implies that Zc, the critical charge below which the three electron atom is not bound, is at most 2. The vanishing electron affinity of He implies that Zc is not less than 2. Hence, Zc=2. To elucidate the approach to the critical charge, we calculated nonrelativistic binding energies for the third electron in the ground state, 1s22s2S, and in the first and second excited states, 1s22p2P and 1s23s2S, for nuclear charges approaching Zc. At this limit the quantum defects for both 2S states are found to approach unity. This implies that the orbital specifying the outer (ns,n=2,3) electron becomes a very diffuse (n-1)s-type orbital, except within the relatively tiny space occupied by the inner two-electron shell. For the 2P state the quantum defect approaches zero both as Z→∞ and as Z→2. An expression for the s-p splitting at Z→2 is suggested, that improves upon earlier results based on energies computed (or measured) at integer values of Z. Rigorous large Z asymptotic expressions for the quantum defects in the 1s2ns2S states are presented, exhibiting the expected mild dependence on the principal quantum number.

  5. Effects of Crossed Electric and Magnetic Fields on Shallow Donor Impurity Binding Energy in a Parabolic Quantum Well

    Institute of Scientific and Technical Information of China (English)

    E. Kasapoglu; H. Sari; I. S(o)kmen

    2004-01-01

    @@ We have calculated variationally the ground state binding energy of a hydrogenic donor impurity in a parabolic quantum well in the presence of crossed electric and magnetic fields. These homogeneous crossed fields are such that the magnetic field is parallel to the heterostructure layers and the electric field is applied perpendicular to the magnetic field. The dependence of the donor impurity binding energy to the well width and the strength of the electric and magnetic fields are discussed. We hope that the obtained results will provide important improvements in device applications, especially for a suitable choice of both fields in the narrow well widths.

  6. Effect of Magnetic Field and Shell Thickness on Binding Energies of a ZnSe/ZnS Core Shell Quantum Dot

    Science.gov (United States)

    Bhat, Bashir Mohi ud din; Parvaiz, Muhammad Shunaid; Sen, Pratima

    2017-02-01

    We investigated the effect of external magnetic field and shell thickness on the binding energies of a ZnSe/ZnS core shell quantum dot. The binding energies were calculated using the variational method within the effective mass approximation and confinement potential. The binding energy of the 2 s and 2 p + states was found to increase with magnetic field. However, the 2 p 0 state was found to be independent of the magnetic field at a shell thickness of 0.5 nm. Degeneracy of the lifted 2 p states was found to occur. The results also showed that the electron binding energy increases at the outset with the increasing shell thickness, and at larger shell thicknesses, the binding energy saturates. The binding energy was found to be decreasing with increasing core diameter and becomes appreciably smaller at core radius of 0.42 nm. The observed results were compared with the previously reported results.

  7. The Shifts of Band Gap and Binding Energies of Titania/Hydroxyapatite Material

    Directory of Open Access Journals (Sweden)

    Nguyen Thi Truc Linh

    2014-01-01

    Full Text Available The titania/hydroxyapatite (TiO2/HAp product was prepared by precipitating hydroxyapatite in the presence of TiO(OH2 gel in the hydrothermal system. The characteristics of the material were determined by using the measurements such as X-ray photoemission spectroscopy (XPS, X-ray diffraction (XRD, diffuse reflectance spectra (DRS, transmission electron microscopy (TEM, scanning electron microscopy (SEM, and energy dispersive X-ray (EDX. The XPS analysis showed that the binding energy values of Ca (2p1/2, 2p3/2, P (2p1/2, 2p3/2, and O 1s levels related to hydroxyapatite phase whereas those of Ti (2p3/2, 2p1/2 levels corresponded with the characterization of titanium (IV in TiO2. The XRD result revealed that TiO2/HAp sample had hydroxyapatite phase, but anatase or rutile phases were not found out. TEM image of TiO2/HAp product showed that the surface of the plate-shaped HAp particles had a lot of smaller particles which were considered as the compound of Ti. The experimental band gap of TiO2/HAp material calculated by the DRS measurement was 3.6 eV, while that of HAp pure was 5.3 eV and that of TiO2 pure was around 3.2 eV. The shift of the band gap energy of TiO2 in the range of 3.2–3.6 eV may be related to the shifts of Ti signals of XPS spectrum.

  8. Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations.

    Science.gov (United States)

    Zhao, Chunfeng; Caplan, David A; Noskov, Sergei Yu

    2010-06-08

    The binding of ligands to protein receptors with high affinity and specificity is central to many cellular processes. The quest for the development of computational models capable of accurately evaluating binding affinity remains one of the main goals of modern computational biophysics. In this work, free energy perturbation/molecular dynamics simulations were used to evaluate absolute and relative binding affinity for three different antidepressants to a sodium-dependent membrane transporter, LeuT, a bacterial homologue of human serotonin and dopamine transporters. Dysfunction of these membrane transporters in mammals has been implicated in multiple diseases of the nervous system, including bipolar disorder and depression. Furthermore, these proteins are key targets for antidepressants including fluoxetine (aka Prozac) and tricyclic antidepressants known to block transport activity. In addition to being clinically relevant, this system, where multiple crystal structures are readily available, represents an ideal testing ground for methods used to study the molecular mechanisms of ligand binding to membrane proteins. We discuss possible pitfalls and different levels of approximation required to evaluate binding affinity, such as the dependence of the computed affinities on the strength of constraints and the sensitivity of the computed affinities to the particular partial charges derived from restrained electrostatic potential fitting of quantum mechanics electrostatic potential. Finally, we compare the effects of different constraint schemes on the absolute and relative binding affinities obtained from free energy simulations.

  9. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.

    Directory of Open Access Journals (Sweden)

    Marharyta Petukh

    2015-07-01

    Full Text Available A new methodology termed Single Amino Acid Mutation based change in Binding free Energy (SAAMBE was developed to predict the changes of the binding free energy caused by mutations. The method utilizes 3D structures of the corresponding protein-protein complexes and takes advantage of both approaches: sequence- and structure-based methods. The method has two components: a MM/PBSA-based component, and an additional set of statistical terms delivered from statistical investigation of physico-chemical properties of protein complexes. While the approach is rigid body approach and does not explicitly consider plausible conformational changes caused by the binding, the effect of conformational changes, including changes away from binding interface, on electrostatics are mimicked with amino acid specific dielectric constants. This provides significant improvement of SAAMBE predictions as indicated by better match against experimentally determined binding free energy changes over 1300 mutations in 43 proteins. The final benchmarking resulted in a very good agreement with experimental data (correlation coefficient 0.624 while the algorithm being fast enough to allow for large-scale calculations (the average time is less than a minute per mutation.

  10. Temperature dependence of the nuclear binding energy: effects on the EOS for hot nuclear matter using different models

    Energy Technology Data Exchange (ETDEWEB)

    Benvenuto, O.G. [La Plata Univ. (Argentina). Fac. of Astron. and Geophys.; Civitarese, O. [Dept. of Physics, Univ. of La Plata (Argentina); Reboiro, M. [Dept. of Physics, Univ. of La Plata (Argentina)

    1997-05-01

    Effects due to the temperature dependence of the nuclear binding energy upon the equation of state (EOS) for hot nuclear matter are studied. Nuclear contributions to the free energy are represented by temperature dependent liquid drop model terms. Phase coexistence is assumed for temperatures of the order of 1 MeV {<=} T {<=} 6 MeV, baryon number densities {rho} of the order of 10{sup -4}fm{sup -3} {<=} {rho} {<=} 10{sup -1}fm{sup -3} and lepton fractions of the order of 0.2 {<=} y{sub 1} {<=} 0.4. It is found that the total pressure of the system is not affected by the temperature dependence of the nuclear free energy, in spite of changes observed in the nuclear pressure due to the different parametrizations used to represent the nuclear binding energy. (orig.).

  11. Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.

    Directory of Open Access Journals (Sweden)

    M Olivia Kim

    2015-10-01

    Full Text Available BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer's disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.

  12. Changes in the zero-point energy of the protons as the source of the binding energy of water to A-phase DNA.

    Science.gov (United States)

    Reiter, G F; Senesi, R; Mayers, J

    2010-10-01

    The measured changes in the zero-point kinetic energy of the protons are entirely responsible for the binding energy of water molecules to A phase DNA at the concentration of 6  water molecules/base pair. The changes in kinetic energy can be expected to be a significant contribution to the energy balance in intracellular biological processes and the properties of nano-confined water. The shape of the momentum distribution in the dehydrated A phase is consistent with coherent delocalization of some of the protons in a double well potential, with a separation of the wells of 0.2 Å.

  13. Effects due to temperature-dependent nuclear binding energies on the equation of state for hot nuclear matter

    Energy Technology Data Exchange (ETDEWEB)

    Benvenuto, O.G. (Facultad de Ciencias Astronomica y Geofisicas, Universidad Nacional de La Plata, La Plata, Buenos Aires (Argentina)); Civitarese, O.; Reboiro, M. (Departamento de Fisica, Universidad Nacional de La Plata, La Plata, Buenos Aires (Argentina))

    1993-05-01

    The influence of finite temperature nuclear effects upon the adiabatic index, for a system of nuclei, nucleons, and leptons, is discussed. It is found that the inclusion of temperature-dependent nuclear binding energies affects the behavior of the adiabats and of the adiabatic index, particularly, at low entropies.

  14. Development of molecular docking-based binding energy to predict the joint effect of BPA and its analogs.

    Science.gov (United States)

    Zhang, Hong-Chang; Hu, Xia-Lin; Yin, Da-Qiang; Lin, Zhi-Fen

    2011-04-01

    A general proposal for predicting the joint effect of endocrine disrupting chemicals by examining binding energy models was developed in this study. 2,2-bis(4-hydroxyphenyl)propane (BPA) and 11 of its analogs were chosen, and the estrogenic activity of each compound was measured by determining its EC50 value using a recombinant gene yeast assay. Binding energies (BEs) were calculated using Surflex-Docking software. The analysis of the relationship between EC50 values and BEs showed that there is a linear correlation between the BEs and EC50 values. Furthermore, the analysis of the given binary and quaternary mixtures of BPA and three of its analogs showed that the joint effects of the mixtures were affected by the proportions of the chemicals in each mixture and their relative binding energy. The correlation between the joint effects of mixtures and the binding energy of the individual compounds has been described using one formula, which can be used to predict the joint effects of other mixtures.

  15. Investigating the relative influences of molecular dimensions and binding energies on diffusivities of guest species inside nanoporous crystalline materials

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2012-01-01

    The primary objective of this article is to investigate the relative influences of molecular dimensions and adsorption binding energies on unary diffusivities of guest species inside nanoporous crystalline materials such as zeolites and metal-organic frameworks (MOFs). The investigations are based o

  16. Measurement of the binding energy of ultracold $^{87}$Rb$^{133}$Cs molecules using an offset-free optical frequency comb

    CERN Document Server

    Molony, Peter K; Gregory, Philip D; Kliese, Russell; Puppe, Thomas; Sueur, C Ruth Le; Aldegunde, Jesus; Hutson, Jeremy M; Cornish, Simon L

    2016-01-01

    We report the binding energy of $^{87}$Rb$^{133}$Cs molecules in their rovibrational ground state measured using an offset-free optical frequency comb based on difference frequency generation technology. We create molecules in the absolute ground state using stimulated Raman adiabatic passage (STIRAP) with a transfer efficiency of 88\\%. By measuring the absolute frequencies of our STIRAP lasers, we find the energy-level difference from an initial weakly-bound Feshbach state to the rovibrational ground state with a resolution of 5 kHz over an energy-level difference of more than 114 THz; this lets us discern the hyperfine splitting of the ground state. Combined with theoretical models of the Feshbach state binding energies and ground-state hyperfine structure, we determine a zero-field binding energy of $h\\times114\\,268\\,135\\,237(5)(50)$ kHz. To our knowledge, this is the most accurate determination to date of the dissociation energy of a molecule.

  17. Measurement of the binding energy of ultracold 87Rb133Cs molecules using an offset-free optical frequency comb

    Science.gov (United States)

    Molony, Peter K.; Kumar, Avinash; Gregory, Philip D.; Kliese, Russell; Puppe, Thomas; Le Sueur, C. Ruth; Aldegunde, Jesus; Hutson, Jeremy M.; Cornish, Simon L.

    2016-08-01

    We report the binding energy of 87Rb133Cs molecules in their rovibrational ground state measured using an offset-free optical frequency comb based on difference frequency generation technology. We create molecules in the absolute ground state using stimulated Raman adiabatic passage (STIRAP) with a transfer efficiency of 88%. By measuring the absolute frequencies of our STIRAP lasers, we find the energy-level difference from an initial weakly bound Feshbach state to the rovibrational ground state with a resolution of ˜5 kHz over an energy-level difference of more than 114 T Hz ; this lets us discern the hyperfine splitting of the ground state. Combined with theoretical models of the Feshbach-state binding energies and ground-state hyperfine structure, we determine a zero-field binding energy of h ×114 268 135.24 (4 )(3 )M Hz . To our knowledge, this is the most accurate determination to date of the dissociation energy of a molecule.

  18. Development of homogeneous binding assays based on fluorescence resonance energy transfer between quantum dots and Alexa Fluor fluorophores.

    Science.gov (United States)

    Nikiforov, Theo T; Beechem, Joseph M

    2006-10-01

    We studied the fluorescence resonance energy transfer (FRET) between quantum dots emitting at 565, 605, and 655 nm as energy donors and Alexa Fluor fluorophores with absorbance maxima at 594, 633, 647, and 680 nm as energy acceptors. As a first step, we prepared covalent conjugates between all three types of quantum dots and each of the Alexa Fluor fluorophores that could act as an energy acceptor. All of these conjugates displayed efficient resonance energy transfer. Then we prepared covalent conjugates of these quantum dots with biotin, fluorescein, and cortisol and established that the binding of these conjugates to suitable Alexa Fluor-labeled antibodies and streptavidin (in the case of biotin) can be efficiently detected by measuring the resonance energy transfer in homogeneous solutions. Finally, based on these observations, competitive binding assays for these three small analytes were developed. The performance of these assays as a function of the degree of labeling of the quantum dots was evaluated. It was found that decreasing the degree of loading of the quantum dots leads to decreases of the limits of detection. The results show the great potential of this FRET system for the development of new homogeneous binding assays.

  19. Simulation of symmetric nuclei and the role of Pauli potential in binding energies

    Energy Technology Data Exchange (ETDEWEB)

    M. Angeles Perez-Garcia, K. Tsushima, A. Valcarce

    2009-05-01

    It is shown that the use of a density dependent effective Pauli potential together with a nucleon-nucleon interaction potential plays a crucial role to reproduce not only the binding energies but also the matter root mean square radii of medium mass range spin-isospin saturated nuclei. This study is performed with a semiclassical Monte Carlo many-body simulation within the context of a simplified nucleon-nucleon interaction to focus on the effect of the genuine correlations due to the fermionic nature of nucleons. The procedure obtained is rather robust and it does not depend on the detailed features of the nucleon-nucleon interaction. For nuclei below saturation the density dependence may be represented in terms either of the nucleon number, $A$, or the associated Fermi momenta. When testing the simulation procedure for idealized "infinite" symmetric nuclear matter within the corresponding range of densities, it turns out that finite size effects affect the Pauli potential strength parametrization in systems up to about 120 particles while remaining approximately stable for larger systems.

  20. Spectroscopy of mesons and proton binding energy in the statistical model with three-quarkonium potentials

    Energy Technology Data Exchange (ETDEWEB)

    Ikhdair, S.M.; Sever, R.; Magdy, M.A. [Middle East Technical Univ., Ankara (Turkey)

    1994-04-01

    The mass spectra of the lowest S, P and D levels of the self-conjugate (Q{bar Q}) and the non-self-conjugate (Q{bar q}) mesons are studied with the three flavour-dependent static quark-antiquark potentials, belong to the class U(r)=a{sub 1}r{sup {gamma}}{minus}a{sub 2}r{sup {minus}{gamma}}+a{sub 3}, for {gamma}=1, 1/2, 3/4 cases. The non-relativistic form of statistical model is used in the calculations. The leptonic decay widths and decay constants of the vector Q{bar Q} and the psuedoscalar Q{bar q} mesons are estimated by considering the improved version of the Van Royen-Weisskopf formula. Moreover, the binding energy, the form factor and the charge radius of the proton have also been calculated. These results are in reasonably good agreement with experimental and theoretical findings. 21 refs., 6 tabs.

  1. Binding energy and mechanical stability of single- and multi-walled carbon nanotube serpentines

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Junhua, E-mail: junhua.zhao@163.com, E-mail: timon.rabczuk@uni-weimar.de [Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, 214122 Wuxi (China); Institute of Structural Mechanics, Bauhaus University, 99423 Weimar (Germany); Lu, Lixin [Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, 214122 Wuxi (China); Rabczuk, Timon, E-mail: junhua.zhao@163.com, E-mail: timon.rabczuk@uni-weimar.de [Institute of Structural Mechanics, Bauhaus University, 99423 Weimar (Germany)

    2014-05-28

    Recently, Geblinger et al. [Nat. Nanotechnol. 3, 195 (2008)] and Machado et al. [Phys. Rev. Lett. 110, 105502 (2013)] reported the experimental and molecular dynamics realization of S-like shaped single-walled carbon nanotubes (CNTs), the so-called CNT serpentines. We reported here results from continuum modeling of the binding energy γ between different single- and multi-walled CNT serpentines and substrates as well as the mechanical stability of the CNT serpentine formation. The critical length for the mechanical stability and adhesion of different CNT serpentines are determined in dependence of E{sub i}I{sub i}, d, and γ, where E{sub i}I{sub i} and d are the CNT bending stiffness and distance of the CNT translation period. Our continuum model is validated by comparing its solution to full-atom molecular dynamics calculations. The derived analytical solutions are of great importance for understanding the interaction mechanism between different single- and multi-walled CNT serpentines and substrates.

  2. High level theoretical study of binding and of the potential energy surface in benzene-hydride system

    Energy Technology Data Exchange (ETDEWEB)

    Coletti, Cecilia, E-mail: ccoletti@unich.it [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy); Re, Nazzareno [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy)

    2012-04-04

    Graphical abstract: In-plane minimum geometries for benzene-H{sup -} non-covalent adducts: linear adduct (left) with the hydride ion hydrogen bonded to one aromatic hydrogen; bifurcated adduct (right), with the hydride ion hydrogen bonded to two adjacent aromatic hydrogens. Highlights: Black-Right-Pointing-Pointer Theoretical study on covalent and non-covalent binding in benzene-hydride. Black-Right-Pointing-Pointer Two non-covalent stable adducts were characterized in the in-plane geometry. Black-Right-Pointing-Pointer Significant sections of the potential energy surface were determined. Black-Right-Pointing-Pointer Formation of a very stable C{sub 6}H{sub 7}{sup -} anion upon covalent binding to carbon. - Abstract: High level ab initio calculations were performed on the interaction of the hydride anion with benzene, a system of potential interest for modelling the interactions occurring in hydrogen rich planetary atmospheres. We investigated both non-covalent and covalent binding, exploring the complete basis set limit using highly correlated MP2 and CCSD(T) levels of theory. Two non-covalent minima on the potential energy surface have been characterized, and found to correspond to moderately strong hydrogen bonding interactions. To gain further insight on the nature of binding, the total interaction energy was decomposed into its physically meaningful components and selected sections of the potential energy surface were calculated. Moreover, we found that H{sup -} can easily covalently bind to one of the carbon atoms of benzene to form a stable C{sub 6}H{sub 7}{sup -} anion, a global minimum on the potential energy surface, characterized by a puckered geometry, with a carbon atom bending out of the benzene plane. A slightly less stable planar C{sub 6}H{sub 7}{sup -} structure was also identified, corresponding to the transition state for the flipping motion of the puckered species.

  3. Why baryons are Yang-Mills magnetic monopoles, validated by nuclear binding energies and proton and neutron masses

    Science.gov (United States)

    Yablon, Jay R.

    2013-10-01

    Evidence is summarized from four recent papers that baryons including protons and neutrons are magnetic monopoles of non-commuting Yang-Mills gauge theories: 1) Protons and neutrons are ``resonant cavities'' with binding energies determined strictly by the masses of the quarks they contain. This is proven true at parts-per million accuracy for each of the 2H, 3H,3He, 4He binding energies and the neutron minus proton mass difference. 2) Respectively, each free proton and neutron contains 7.64 MeV and 9.81 MeV of mass/energy used to confine its quarks. When these nucleons bind, some, never all, of this energy is released and the mass deficit goes into binding. The balance continues to confine quarks. 56Fe releases 99.8429% of this energy for binding, more than any other nuclide. 3) Once we consider the Fermi vev one also finds an entirely theoretical explanation of proton and neutron masses, which also connects within experimental errors to the CKM quark mixing angles. 4) A related GUT explains fermion generation replication based on generator loss during symmetry breaking, and answers Rabi's question ``who ordered this?'' 5) Nuclear physics is governed by combining Maxwell's two classical equations into one equation using non-commuting gauge fields in view of Dirac theory and Fermi-Dirac-Pauli Exclusion. 6) Atoms themselves are core magnetic charges (nucleons) paired with orbital electric charges (electrons and elusive neutrinos), with the periodic table itself revealing an electric/magnetic symmetry of Maxwell's equations often pondered but heretofore unrecognized for a century and a half.

  4. Subsite binding energies of an exo-polygalacturonase using isothermal titration calorimetry

    Science.gov (United States)

    Thermodynamic parameters for binding of a series of galacturonic acid oligomers to an exo-polygalacturonase, RPG16 from Rhizopus oryzae, were determined by isothermal titration calorimetry. Binding of oligomers varying in chain length from two to five galacturonic acid residues is an exothermic proc...

  5. Binding and Adsorption Energies of Heavy Metal Ions with Hapli-Udic Argosol and Ferri-Udic Argosol Particles

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Gibbs free binding energy and adsorption energy between cations and charged soil particles were used to evaluate the interactions between ions and soil particles. The distribution of Gibbs free adsorption energies could not be determined experimentally before the development of Wien effect measurements in dilute soil suspensions. In the current study, energy relationships between heavy metal ions and particles of Hapli-Udic Argosol (Alfisol) and Ferri-Udic Argosol were inferred from Wien effect measurements in dilute suspensions of homoionic soil particles (< 2 μm) of the two soils, which were saturated with ions of five heavy metals, in deionized water. The mean Gibbs free binding energies of the heavy metal ions with Hapli-Udic Argosol and Ferri-Udic Argosol particles diminished in the order of Pb2+>Cd2+>Cu2+> Zn2+ >Cr3+, where the range of binding energies for Hapli-Udic Argosol (7.25-9.32 kJ mol-1) was similar to that for Ferri-Udic Argosol (7.43-9.35 kJ mol-1). The electrical field-dependent mean Gibbs free adsorption energies of these heavy metal ions for Hapli-Udic Argosol and for Ferri-Udic Argosol descended in the order: Cu2+≥ Cd2+≥ Pb2+ > Zn2+>Cr3+,and Cd2+ >Cu2+>Pb2+>Zn2+>Cr3+, respectively. The mean Gibbs free adsorption energies of Cu2+, Zn2+, Cd2+,Pb2+, and Cr3+ at a field strength of 200 kV cm-1, for example, were in the range of 0.8-3.2 kJ mol-1 for the two soils.

  6. Determination of the cationic amphiphilic drug-DNA binding mode and DNA-assisted fluorescence resonance energy transfer amplification.

    Science.gov (United States)

    Yaseen, Zahid; Banday, Abdul Rouf; Hussain, Mohammed Aamir; Tabish, Mohammad; Kabir-ud-Din

    2014-03-25

    Understanding the mechanism of drug-DNA binding is crucial for predicting the potential genotoxicity of drugs. Agarose gel electrophoresis, absorption, steady state fluorescence, and circular dichroism have been used in exploring the interaction of cationic amphiphilic drugs (CADs) such as amitriptyline hydrochloride (AMT), imipramine hydrochloride (IMP), and promethazine hydrochloride (PMT) with calf thymus or pUC19 DNA. Agarose gel electrophoresis assay, along with absorption and steady state fluorescence studies, reveal interaction between the CADs and DNA. A comparative study of the drugs with respect to the effect of urea, iodide induced quenching, and ethidium bromide (EB) exclusion assay reflects binding of CADs to the DNA primarily in an intercalative fashion. Circular dichroism data also support the intercalative mode of binding. Besides quenching, there is fluorescence exchange energy transfer (FRET) in between CADs and EB using DNA as a template.

  7. Molecular dynamics simulation of tryptophan hydroxylase-1: binding modes and free energy analysis to phenylalanine derivative inhibitors.

    Science.gov (United States)

    Zhong, Hao; Huang, Wei; He, Gu; Peng, Cheng; Wu, Fengbo; Ouyang, Liang

    2013-05-10

    Serotonin is a neurotransmitter that modulates many central and peripheral functions. Tryptophan hydroxylase-1 (TPH1) is a key enzyme of serotonin synthesis. In the current study, the interaction mechanism of phenylalanine derivative TPH1 inhibitors was investigated using molecular dynamics (MD) simulations, free energy calculations, free energy decomposition analysis and computational alanine scanning. The predicted binding free energies of these complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals and electrostatics interaction contributions are important in distinguishing the binding affinities of these inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the naphthalene substituent could form different binding patterns with protein, yet lead to similar inhibitory potency. The combination of different molecular modeling techniques is an efficient way to interpret the interaction mechanism of inhibitors and our work could provide valuable information for the TPH1 inhibitor design in the future.

  8. Molecular Dynamics Simulation of Tryptophan Hydroxylase-1: Binding Modes and Free Energy Analysis to Phenylalanine Derivative Inhibitors

    Directory of Open Access Journals (Sweden)

    Liang Ouyang

    2013-05-01

    Full Text Available Serotonin is a neurotransmitter that modulates many central and peripheral functions. Tryptophan hydroxylase-1 (TPH1 is a key enzyme of serotonin synthesis. In the current study, the interaction mechanism of phenylalanine derivative TPH1 inhibitors was investigated using molecular dynamics (MD simulations, free energy calculations, free energy decomposition analysis and computational alanine scanning. The predicted binding free energies of these complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals and electrostatics interaction contributions are important in distinguishing the binding affinities of these inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the naphthalene substituent could form different binding patterns with protein, yet lead to similar inhibitory potency. The combination of different molecular modeling techniques is an efficient way to interpret the interaction mechanism of inhibitors and our work could provide valuable information for the TPH1 inhibitor design in the future.

  9. Donor Binding Energy in GaAs/Ga1-x AlxAs Quantum Well: the Laser Field and Temperature Effects

    Institute of Scientific and Technical Information of China (English)

    WEI Shu-Yi; HOU Wen-Xiu; CHEN Xiao-Yang; XIA Cong-Xin

    2013-01-01

    Based on the effective-mass approximation theory and variational method,the laser field and temperature effects on the ground-state donor binding energy in the GaAs/Ga1-xAlxAs quantum well (QW) are investigated.Numerical results show that the donor binding energy depends on the impurity position,laser parameter,temperature,Al composition,and well width.The donor binding energy is decreased when the laser field and temperature are increased in the QW for any impurity position and QW parameter case.Moreover,the laser field has an obvious influence on the donor binding energy of impurity located at the vicinity of the QW center.In addition,our results also show that the donor binding energy decreases (or increases) as the well width (or Al composition x) increases in the QW.

  10. Binding energy referencing for XPS in alkali metal-based battery materials research (I): Basic model investigations

    Energy Technology Data Exchange (ETDEWEB)

    Oswald, S., E-mail: s.oswald@ifw-dresden.de

    2015-10-01

    Highlights: • We point to a not seriously solved conflict in energy scale referencing of Li metal samples in XPS. • Model experiments at Li-, Na-metal and Li-doped HOPG samples were used to classify the effects. • Binding energy shifts up to 3 eV are observed when the alkaline metal is present in metallic state. • A phenomenological explanation based on an electrostatic interaction is suggested. • Consequences for energy scale correction depending on the kind of surface species are followed. - Abstract: For the investigation of chemical changes in Li- and Na-ion battery electrode systems, X-ray photoelectron spectroscopy (XPS) is a well-accepted method. Charge compensation and referencing of the binding energy (BE) scale is necessary to account for the involved mostly non-conducting species. Motivated by a conflict in energy scale referencing of Li-metal samples discussed earlier by several authors, further clarifying experimental results on several Li containing reference materials are presented and extended by similar experiments for Na. When correlating the peak positions of characteristic chemical species in all the different prepared model sample states, there seems to be a systematic deviation in characteristic binding energies of several eV if lithium is present in its metallic state. Similar results were found for sodium. The observations are furthermore confirmed by the implementation of inert artificial energy reference material, such as implanted argon or deposited gold. The behavior is associated with the high reactivity of metallic lithium and a phenomenological explanation is proposed for the understanding of the observations. Consequences for data interpretation in Li-ion battery research will be discussed for various applications in part (II)

  11. Magnetic field-dependent of binding energy in GaN/InGaN/GaN spherical QDQW nanoparticles

    Science.gov (United States)

    El Ghazi, Haddou; Jorio, Anouar; Zorkani, Izeddine

    2013-10-01

    Simultaneous study of magnetic field and impurity's position effects on the ground-state shallow-donor binding energy in GaN│InGaN│GaN (core│well│shell) spherical quantum dot-quantum well (SQDQW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated within the framework of the effective-mass approximation and an infinite deep potential describing the quantum confinement effect. A Ritz variational approach is used taking into account of the electron-impurity correlation and the magnetic field effect in the trial wave-function. It appears that the binding energy depends strongly on the external magnetic field, the impurity's position and the structure radius. It has been found that: (i) the magnetic field effect is more marked in large layer than in thin layer and (ii) it is more pronounced in the spherical layer center than in its extremities.

  12. Energy coupling to periplasmic binding protein-dependent transport systems: stoichiometry of ATP hydrolysis during transport in vivo.

    OpenAIRE

    Mimmack, M L; Gallagher, M P; Pearce, S R; Hyde, S C; Booth, I R; Higgins, C F

    1989-01-01

    Periplasmic binding protein-dependent transport systems mediate the accumulation of many diverse substrates in prokaryotic cells. Similar transport systems, including the P-glycoprotein responsible for multidrug resistance in human tumors, are also found in eukaryotes. The mechanism by which energy is coupled to the accumulation of substrate by these transport systems has been controversial. In this paper we demonstrate that ATP hydrolysis occurs in vivo concomitantly with transport. These da...

  13. Fluorescence Resonance Energy Transfer Imaging Reveals that Chemokine-Binding Modulates Heterodimers of CXCR4 and CCR5 Receptors

    OpenAIRE

    2008-01-01

    BACKGROUND: Dimerization has emerged as an important feature of chemokine G-protein-coupled receptors. CXCR4 and CCR5 regulate leukocyte chemotaxis and also serve as a co-receptor for HIV entry. Both receptors are recruited to the immunological synapse during T-cell activation. However, it is not clear whether they form heterodimers and whether ligand binding modulates the dimer formation. METHODOLOGY/PRINCIPAL FINDINGS: Using a sensitive Fluorescence Resonance Energy Transfer (FRET) imaging ...

  14. Total energy calculation of perovskite, BaTiO3, by self-consistent tight binding method

    Indian Academy of Sciences (India)

    B T Cong; P N A Huy; P K Schelling; J W Halley

    2003-01-01

    We present results of numerical computation on some characteristics of BaTiO3 such as total energy, lattice constant, density of states, band structure etc using self-consistent tight binding method. Besides strong Ti–O bond between 3 on titanium and 2 orbital on oxygen states, we also include weak hybridization between the Ba 6 and O 2 states. The results are compared with those of other more sophisticated methods.

  15. Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

    Directory of Open Access Journals (Sweden)

    Sentot Joko Raharjo

    2014-01-01

    Full Text Available To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX, the three-dimensional (3D structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli alcohol isomers. Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking tools by Hex 8.0. Interactions were further visualized by using Discovery Studio Client 3.5 software tool. The binding energy of molecular interaction was calculated by AMBER12 and Virtual Molecular Dynamic 1.9.1 software. The analysis of the alpha-Patchouli alcohol isomer compounds showed that all alpha-Patchouli alcohol isomers were suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent of alpha-Patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117 was suggested as candidate for a selective COX-1 inhibitor and CID521903 as nonselective COX-1/COX-2.

  16. Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context.

    Science.gov (United States)

    Homeyer, Nadine; Stoll, Friederike; Hillisch, Alexander; Gohlke, Holger

    2014-08-12

    Correctly ranking compounds according to their computed relative binding affinities will be of great value for decision making in the lead optimization phase of industrial drug discovery. However, the performance of existing computationally demanding binding free energy calculation methods in this context is largely unknown. We analyzed the performance of the molecular mechanics continuum solvent, the linear interaction energy (LIE), and the thermodynamic integration (TI) approach for three sets of compounds from industrial lead optimization projects. The data sets pose challenges typical for this early stage of drug discovery. None of the methods was sufficiently predictive when applied out of the box without considering these challenges. Detailed investigations of failures revealed critical points that are essential for good binding free energy predictions. When data set-specific features were considered accordingly, predictions valuable for lead optimization could be obtained for all approaches but LIE. Our findings lead to clear recommendations for when to use which of the above approaches. Our findings also stress the important role of expert knowledge in this process, not least for estimating the accuracy of prediction results by TI, using indicators such as the size and chemical structure of exchanged groups and the statistical error in the predictions. Such knowledge will be invaluable when it comes to the question which of the TI results can be trusted for decision making.

  17. Global analysis of steady-state energy transfer measurements in membranes: resolution of structural and binding parameters.

    Science.gov (United States)

    Domanov, Yegor A; Gorbenko, Galina P; Molotkovsky, Julian G

    2004-01-01

    A method has been developed allowing structural and binding parameters to be recovered by global analysis of two-dimensional array of steady-state RET data in the special case where energy acceptors distribute between aqueous and lipid phases while donors are embedded in the membrane at a known depth. To test the validity of this approach, correlation and error analyses have been performed using simulated data. To exemplify the method application to the membrane studies, energy transfer from anthrylvinyl-labeled phosphatidylcholine incorporated into mixed phosphatidylcholine/cardiolipin unilamellar vesicles to heme group of cytochrome c is analyzed.

  18. A structure-based design of new C2- and C13-substituted taxanes: tubulin binding affinities and extended quantitative structure-activity relationships using comparative binding energy (COMBINE) analysis.

    Science.gov (United States)

    Coderch, Claire; Tang, Yong; Klett, Javier; Zhang, Shu-En; Ma, Yun-Tao; Shaorong, Wang; Matesanz, Ruth; Pera, Benet; Canales, Angeles; Jiménez-Barbero, Jesús; Morreale, Antonio; Díaz, J Fernando; Fang, Wei-Shuo; Gago, Federico

    2013-05-14

    Ten novel taxanes bearing modifications at the C2 and C13 positions of the baccatin core have been synthesized and their binding affinities for mammalian tubulin have been experimentally measured. The design strategy was guided by (i) calculation of interaction energy maps with carbon, nitrogen and oxygen probes within the taxane-binding site of β-tubulin, and (ii) the prospective use of a structure-based QSAR (COMBINE) model derived from an earlier series comprising 47 congeneric taxanes. The tubulin-binding affinity displayed by one of the new compounds (CTX63) proved to be higher than that of docetaxel, and an updated COMBINE model provided a good correlation between the experimental binding free energies and a set of weighted residue-based ligand-receptor interaction energies for 54 out of the 57 compounds studied. The remaining three outliers from the original training series have in common a large unfavourable entropic contribution to the binding free energy that we attribute to taxane preorganization in aqueous solution in a conformation different from that compatible with tubulin binding. Support for this proposal was obtained from solution NMR experiments and molecular dynamics simulations in explicit water. Our results shed additional light on the determinants of tubulin-binding affinity for this important class of antitumour agents and pave the way for further rational structural modifications.

  19. Effects of low-energy excitations on spectral properties at higher binding energy: the metal-insulator transition of VO(2).

    Science.gov (United States)

    Gatti, Matteo; Panaccione, Giancarlo; Reining, Lucia

    2015-03-20

    The effects of electron interaction on spectral properties can be understood in terms of coupling between excitations. In transition-metal oxides, the spectral function close to the Fermi level and low-energy excitations between d states have attracted particular attention. In this work we focus on photoemission spectra of vanadium dioxide over a wide (10 eV) range of binding energies. We show that there are clear signatures of the metal-insulator transition over the whole range due to a cross coupling of the delocalized s and p states with low-energy excitations between the localized d states. This coupling can be understood by advanced calculations based on many-body perturbation theory in the GW approximation. We also advocate the fact that tuning the photon energy up to the hard-x-ray range can help to distinguish fingerprints of correlation from pure band-structure effects.

  20. Binding energy and dephasing of biexcitons in In0.18Ga0.82As/GaAs single quantum wells

    DEFF Research Database (Denmark)

    Borri, Paola; Langbein, Wolfgang Werner; Hvam, Jørn Märcher;

    1999-01-01

    Biexciton binding energies and biexciton dephasing in In0.18Ga0.82As/GaAs single quantum wells have been measured by time-integrated and spectrally resolved four-wave mixing. The biexciton binding energy increases from 1.5 to 2.6 meV for well widths increasing from 1 to 4 nm. The ratio between...... exciton and biexciton binding energy changes from 0.23 to 0.3 with increasing inhomogeneous broadening, corresponding to increasing well width. From the temperature dependence of the exciton and biexciton four-wave mixing signal decay, we have deduced the acoustic-phonon scattering of the exciton...

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

    Science.gov (United States)

    Wang, Yeng-Tseng; Chuang, Lea-Yea

    2015-01-01

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

  2. Internal field induced exciton binding energy and the optical transition in a strained Mg based II–VI quantum well

    Energy Technology Data Exchange (ETDEWEB)

    Elangovan, P. [Department of Physics, Maamallan Institute of Technology, Chennai 602105 (India); John Peter, A., E-mail: a.john.peter@gmail.com [Department of Physics, Government Arts College, Melur 625 106. Madurai (India); Kyoo Yoo, Chang [Center for Environmental Studies/Green Energy Center, Deptartment of Environmental Science and Engineering, College of Engineering, Kyung Hee University, Seocheon-dong 1, Giheung-gu, Yongin-Si, Gyeonggi-Do, 446-701 (Korea, Republic of)

    2013-11-15

    Binding energy of an exciton in a wurtzite ZnO/Zn{sub 1−x}Mg{sub x}O strained quantum well is investigated theoretically in which the strong built-in electric field due to the spontaneous and piezoelectric polarizations is included. Numerical calculations are performed using variational procedure within the single band effective mass approximation by varying the Mg composition in the barrier. The exciton oscillator strength and the exciton lifetime for radiative recombination as functions of well width and Mg content have been computed. The internal field induced interband emission energy of strained ZnO/Zn{sub 1−x}Mg{sub x}O well is investigated with the various structural parameters. The total optical absorption coefficients and the changes of refractive index as a function of normalized photon energy in the presence of built-in internal field are analyzed. The result shows that the strong built-in electric field has influence on the oscillator strength and the recombination life time of the exciton. The optical absorption coefficients and the refractive index changes strongly depend on Mg composition. The occurred blue shift of the resonant peak due to the incorporation of Mg ions will give the information about the variation of two energy levels in the quantum well. -- Highlights: • Binding energy of an exciton in a wurtzite ZnO/Zn{sub 1−x}Mg{sub x}O strained quantum well is investigated. • The built-in internal fields due to the spontaneous and piezoelectric polarizations are included. • The oscillator strength and the exciton lifetime for radiative recombination are computed. • The internal field induced transition energy of strained ZnO/Zn{sub 1−x}Mg{sub x}O well is investigated. • The results show that the nonlinear optical properties strongly depend on Mg composition.

  3. Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology

    Science.gov (United States)

    Eid, Sameh; Saleh, Noureldin; Zalewski, Adam; Vedani, Angelo

    2014-12-01

    Carbohydrates play a key role in a variety of physiological and pathological processes and, hence, represent a rich source for the development of novel therapeutic agents. Being able to predict binding mode and binding affinity is an essential, yet lacking, aspect of the structure-based design of carbohydrate-based ligands. We assembled a diverse data set comprising 273 carbohydrate-protein crystal structures with known binding affinity and evaluated the prediction accuracy of a large collection of well-established scoring and free-energy functions, as well as combinations thereof. Unfortunately, the tested functions were not capable of reproducing binding affinities in the studied complexes. To simplify the complex free-energy surface of carbohydrate-protein systems, we classified the studied proteins according to the topology and solvent exposure of the carbohydrate-binding site into five distinct categories. A free-energy model based on the proposed classification scheme reproduced binding affinities in the carbohydrate data set with an r 2 of 0.71 and root-mean-squared-error of 1.25 kcal/mol ( N = 236). The improvement in model performance underlines the significance of the differences in the local micro-environments of carbohydrate-binding sites and demonstrates the usefulness of calibrating free-energy functions individually according to binding-site topology and solvent exposure.

  4. Probing inter- and intrachain Zhang-Rice excitons in Li2CuO2 and determining their binding energy

    Science.gov (United States)

    Monney, Claude; Bisogni, Valentina; Zhou, Ke-Jin; Kraus, Roberto; Strocov, Vladimir N.; Behr, Günter; Drechsler, Stefan-Ludwig; Rosner, Helge; Johnston, Steve; Geck, Jochen; Schmitt, Thorsten

    2016-10-01

    Cuprate materials, such as those hosting high-temperature superconductivity, represent a famous class of materials where the correlations between the strongly entangled charges and spins produce complex phase diagrams. Several years ago, the Zhang-Rice singlet was proposed as a natural quasiparticle in hole-doped cuprates. The occurrence and binding energy of this quasiparticle, consisting of a pair of bound holes with antiparallel spins on the same CuO4 plaquette, depends on the local electronic interactions, which are fundamental quantities for understanding the physics of the cuprates. Here, we employ state-of-the-art resonant inelastic x-ray scattering (RIXS) to probe the correlated physics of the CuO4 plaquettes in the quasi-one-dimensional chain cuprate Li2CuO2 . By tuning the incoming photon energy to the O K edge, we populate bound states related to the Zhang-Rice quasiparticles in the RIXS process. Both intra- and interchain Zhang-Rice singlets are observed and their occurrence is shown to depend on the nearest-neighbor spin-spin correlations, which are readily probed in this experiment. We also extract the binding energy of the Zhang-Rice singlet and identify the Zhang-Rice triplet excitation in the RIXS spectra.

  5. Roles of binding energy and diffusion length of singlet and triplet excitons in organic heterojunction solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Narayan, Monishka Rita [Centre for Renewable Energy and Low Emission Technology, Charles Darwin University, Darwin, NT 0909 (Australia); Singh, Jai [School of Engineering and IT, Charles Darwin University, Darwin, NT 0909 (Australia)

    2012-12-15

    The influence of binding energy and diffusion length on the dissociation of excitons in organic solids is studied. The binding energy and excitonic Bohr radius of singlet and triplet excitons are calculated and compared using the dissociation energy of 0.3 eV, which is provided by the lowest unoccupied molecular orbital offset in heterojunction organic solar cells. A relation between the diffusion coefficient and diffusion length of singlet and triplet excitons is derived using the Foerster and Dexter transfer processes and are plotted as a function of the donor-acceptor separation. The diffusion length reduces nearly to a zero if the distance between donor and acceptor is increased to more than 1.5 nm. It is found that the donor-acceptor separation needs to be {<=} 1.5 nm for easy dissociation on singlet excitons leading to better conversion efficiency in heterojunction organic solar cells. (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  6. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis.

    Science.gov (United States)

    Wang, Qiantao; Edupuganti, Ramakrishna; Tavares, Clint D J; Dalby, Kevin N; Ren, Pengyu

    2015-01-01

    A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r (2) coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r (2) of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.

  7. Alkali metal cation-hexacyclen complexes: effects of alkali metal cation size on the structure and binding energy.

    Science.gov (United States)

    Austin, C A; Rodgers, M T

    2014-07-24

    Threshold collision-induced dissociation (CID) of alkali metal cation-hexacyclen (ha18C6) complexes, M(+)(ha18C6), with xenon is studied using guided ion beam tandem mass spectrometry techniques. The alkali metal cations examined here include: Na(+), K(+), Rb(+), and Cs(+). In all cases, M(+) is the only product observed, corresponding to endothermic loss of the intact ha18C6 ligand. The cross-section thresholds are analyzed to extract zero and 298 K M(+)-ha18C6 bond dissociation energies (BDEs) after properly accounting for the effects of multiple M(+)(ha18C6)-Xe collisions, the kinetic and internal energy distributions of the M(+)(ha18C6) and Xe reactants, and the lifetimes for dissociation of the activated M(+)(ha18C6) complexes. Ab initio and density functional theory calculations are used to determine the structures of ha18C6 and the M(+)(ha18C6) complexes, provide molecular constants necessary for the thermodynamic analysis of the energy-resolved CID data, and theoretical estimates for the M(+)-ha18C6 BDEs. Calculations using a polarizable continuum model are also performed to examine solvent effects on the binding. In the absence of solvent, the M(+)-ha18C6 BDEs decrease as the size of the alkali metal cation increases, consistent with the noncovalent nature of the binding in these complexes. However, in the presence of solvent, the ha18C6 ligand exhibits selectivity for K(+) over the other alkali metal cations. The M(+)(ha18C6) structures and BDEs are compared to those previously reported for the analogous M(+)(18-crown-6) and M(+)(cyclen) complexes to examine the effects of the nature of the donor atom (N versus O) and the number donor atoms (six vs four) on the nature and strength of binding.

  8. Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to C-C chemokine receptor-2 (CCR2).

    Science.gov (United States)

    Chavan, Swapnil; Pawar, Shirishkumar; Singh, Rajesh; Sobhia, M Elizabeth

    2012-05-01

    The C-C chemokine receptor 2 (CCR2) was proved as a multidrug target in many diseases like diabetes, inflammation and AIDS, but rational drug design on this target is still lagging behind as the information on the exact binding site and the crystal structure is not yet available. Therefore, for a successful structure-based drug design, an accurate receptor model in ligand-bound state is necessary. In this study, binding-site residues of CCR2 was determined using in silico alanine scanning mutagenesis and the interactions between TAK-779 and the developed homology model of CCR2. Molecular dynamic simulation and Molecular Mechanics-Generalized Born Solvent Area method was applied to calculate binding free energy difference between the template and mutated protein. Upon mutating 29 amino acids of template protein and comparison of binding free energy with wild type, six residues were identified as putative hot spots of CCR2.

  9. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given.

  10. A search for lowest energy structures of ZnS quantum dots: Genetic algorithm tight-binding study.

    Science.gov (United States)

    Pal, Sougata; Sharma, Rahul; Goswami, Biplab; Sarkar, Pranab; Bhattacharyya, S P

    2009-06-07

    The lowest energy structures of ZnS quantum dots of different sizes have been determined by an unbiased search using genetic algorithm (GA) coupled with the density-functional tight-binding method. The GA search converges to a rather new ringlike configurations of ZnS quantum dots. We have studied the structural, electronic, and optical properties of these ringlike clusters and compared these properties with those of other reported structures of ZnS quantum dots, namely, hollow, zinc-blende, wurtzite, and rocksalt structures.

  11. Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

    experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated...... the free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....

  12. Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

    Science.gov (United States)

    Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

    2014-11-20

    Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  13. Fluorescence resonance energy transfer imaging reveals that chemokine-binding modulates heterodimers of CXCR4 and CCR5 receptors.

    Directory of Open Access Journals (Sweden)

    Nilgun Isik

    Full Text Available BACKGROUND: Dimerization has emerged as an important feature of chemokine G-protein-coupled receptors. CXCR4 and CCR5 regulate leukocyte chemotaxis and also serve as a co-receptor for HIV entry. Both receptors are recruited to the immunological synapse during T-cell activation. However, it is not clear whether they form heterodimers and whether ligand binding modulates the dimer formation. METHODOLOGY/PRINCIPAL FINDINGS: Using a sensitive Fluorescence Resonance Energy Transfer (FRET imaging method, we investigated the formation of CCR5 and CXCR4 heterodimers on the plasma membrane of live cells. We found that CCR5 and CXCR4 exist as constitutive heterodimers and ligands of CCR5 and CXCR4 promote different conformational changes within these preexisting heterodimers. Ligands of CCR5, in contrast to a ligand of CXCR4, induced a clear increase in FRET efficiency, indicating that selective ligands promote and stabilize a distinct conformation of the heterodimers. We also found that mutations at C-terminus of CCR5 reduced its ability to form heterodimers with CXCR4. In addition, ligands induce different conformational transitions of heterodimers of CXCR4 and CCR5 or CCR5(STA and CCR5(Delta4. CONCLUSIONS/SIGNIFICANCE: Taken together, our data suggest a model in which CXCR4 and CCR5 spontaneously form heterodimers and ligand-binding to CXCR4 or CCR5 causes different conformational changes affecting heterodimerization, indicating the complexity of regulation of dimerization/function of these chemokine receptors by ligand binding.

  14. Binding energy and work function of organic electrode materials phenanthraquinone, pyromellitic dianhydride and their derivatives adsorbed on graphene.

    Science.gov (United States)

    Yu, Yang-Xin

    2014-09-24

    Electroactive organic compounds are a novel group of green cathode materials for rechargeable metal-ion batteries. However, the organic battery life is short because the organic compounds can be dissolved by nonaqueous electrolytes. Here a comparative investigation of phenanthraquinone (PQ), pyromellitic dianhydride (PMDA) and their derivatives, i.e., benzo[1,2-b:4,3-b']difuran-4,5-dione (BDFD), benzo[1,2-b:4,3-b']dithiophene-4,5-quinone (BDTQ), 3,8-phenanthroline-5,6-dione (PAD), pyromellitic dithioanhydride (PMDT), pyromellitic diimide (PMDI) and 1,4,5,8-anthracenetetrone (ATO), adsorbed on graphene is performed using a density functional theory (DFT) with a van der Waals (vdW) dispersion-correction. The computed results show a strong physisorption with the binding energies between 1.10 and 1.56 eV. A sequence of the calculated binding energies from weak to strong is found to be BDFD work functions for the nanocomposites are found to be strongly affected by the work function of each organic compound. To understand the DFT results, a novel simple expression is proposed to predict the work function of the nanocomposites from the interfacial dipole and the work functions of the isolated graphene nanosheet and organic molecules. The predicted work functions for the nanocomposites from the new equation agree quite well with the values calculated from the vdW dispersion-corrected DFT.

  15. Positive XPS binding energy shift of supported Cu{sub N}-clusters governed by initial state effects

    Energy Technology Data Exchange (ETDEWEB)

    Peters, S.; Peredkov, S. [Technische Universität Berlin, IOAP, Strasse des 17. Juni 135, 10623 Berlin (Germany); Al-Hada, M. [Department of Physics, College of Education and Linguistics, University of Amran (Yemen); Neeb, M., E-mail: matthias.neeb@helmholtz-berlin.de [Helmholtz-Zentrum Berlin, Wilhelm-Conrad-Röntgen-Campus Adlershof, Elektronenspeicherring BESSY II, Albert-Einstein-Straße 15, 12489 Berlin (Germany); Eberhardt, W. [Technische Universität Berlin, IOAP, Strasse des 17. Juni 135, 10623 Berlin (Germany); DESY, Center for Free Electron Laser Science (CFEL), Notkestr. 85, 22607 Hamburg (Germany)

    2014-01-01

    Highlights: • Size dependent initial and final state effects of mass-selected deposited clusters. • Initial state effect dominates positive XPS shift in supported Cu-clusters. • Size dependent Coulomb correlation shift in the Auger final state of Cu cluster. • Size-dependent Auger parameter analysis. • Positive XPS shift differs from negative surface core level shift in crystalline copper. - Abstract: An initial state effect is established as origin for the positive 2p core electron binding energy shift found for Cu{sub N}-clusters supported by a thin silica layer of a p-doped Si(1 0 0) wafer. Using the concept of the Auger parameter and taking into account the usually neglected Coulomb correlation shift in the Auger final state (M{sub 4,5}M{sub 4,5}) it is shown that the initial state shift is comparable to the measured XPS shift while the final state relaxation shift contributes only marginally to the binding energy shift. The cluster results differ from the negative surface core-level shift of crystalline copper which has been explained in terms of a final state relaxation effect.

  16. What can be learned from binding energy differences about nuclear structure: the example of delta V_{pn}

    CERN Document Server

    Bender, Michael

    2011-01-01

    We perform an analysis of a binding energy difference called delta V_{pn}(N,Z) =- 1/4(E(Z,N)-E(Z,N-2)-E(Z-2,N)+ E(Z-2,N-2) in the framework of a realistic nuclear model. Using the angular-momentum and particle-number projected generator coordinate method and the Skyrme interaction SLy4, we analyze the contribution brought to delta V_{pn} by static deformation and dynamic fluctuations around the mean-field ground state. Our method gives a good overall description of delta V_{pn} throughout the chart of nuclei with the exception of the anomaly related to the Wigner energy along the N=Z line. The main conclusions of our analysis are that (i) the structures seen in the systematics of delta V_{pn} throughout the chart of nuclei can be easily explained combining a smooth background related to the symmetry energy and correlation energies due to deformation and collective fluctuations; (ii) the characteristic pattern of delta V_{pn} around a doubly-magic nucleus is a trivial consequence of the asymmetric definition o...

  17. Binding of oxygen with titanium dioxide on singlet potential energy surface: An ab initio investigation

    Science.gov (United States)

    Bogdanchikov, Georgii A.; Baklanov, Alexey V.

    2017-01-01

    Ab initio calculations have been carried out to investigate interaction of titanium dioxide TiO2 with oxygen O2 in ground triplet and excited singlet states. On a singlet potential energy surface (PES) formation of a stable compound of titanium peroxide TiO4 is revealed which should appear in reaction of TiO2 with singlet oxygen without activation barrier. This peroxide is lower in energy than the ground state of two individual molecules TiO2 + 3O2 by 34.6 kcal/mol. Location of conical intersection between triplet and singlet PESs of TiO2sbnd O2 is also investigated.

  18. Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes

    Science.gov (United States)

    Chu, Wen-Ting; Wang, Jin

    2016-06-01

    Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the “hot-spot” within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design.

  19. Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

    Energy Technology Data Exchange (ETDEWEB)

    Nakano, C. Masato [Flintridge Preparatory School, La Canada Flintridge, California 91011 (United States); Ma, Heng; Wei, Tao, E-mail: twei@lamar.edu [Dan F. Smith Department of Chemical Engineering, Lamar University, Beaumont, Texas 77710 (United States)

    2015-04-13

    Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the other hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.

  20. Binding Energy of D- and D0 Centers Confined by Spherical Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    BAO Yuan-Peng; XIE Wen-Fang

    2008-01-01

    We study a negative donor center, a neutral donor in a spherical Gaussian potential quantum dot by using the matrix diagonalization of Hamiltonian within the effective-mass approximation. We calculate the energy E(D-) as functions of Gaussian potential size and depth, the same calculations as performed with the parabolic approximation. The dependence of the ground state of the neutral shallow donor and the negatively charged donor on the dot size and the potential depth is investigated.

  1. Amine basicity (pKb) controls the analyte binding energy on single walled carbon nanotube electronic sensor arrays.

    Science.gov (United States)

    Lee, Chang Young; Strano, Michael S

    2008-02-06

    A wide range of analytes adsorb irreversibly to the surfaces of single walled carbon nanotube electronic networks typically used as sensors or thin-film transistors, although to date, the mechanism is not understood. Using thionyl chloride as a model electron-withdrawing adsorbate, we show that reversible adsorption sites can be created on the nanotube array via noncovalent functionalization with amine-terminated molecules of pKa nanotube network comprising single, largely unbundled nanotubes, near the electronic percolation threshold is required for the effective conversion to a reversibly binding array. By examining 11 types of amine-containing molecules, we show that analyte adsorption is largely affected by the basicity (pKb) of surface groups. The binding energy of the analyte is apparently reduced by its adsorption on the surface chemical groups instead of directly on the SWNT array itself. This mediated adsorption mechanism is supported by X-ray photoelectron spectroscopy (XPS) and molecular potential calculations. Reversible detection with no active regeneration at the parts-per-trillion level is demonstrated for the first time by creating a higher adsorption site density with a polymer amine, such as polyethyleneimine (PEI). Last, we demonstrate that this transition to reversibility upon surface functionalization is a general phenomenon.

  2. ADMET, Docking studies & binding energy calculations of some Novel ACE - inhibitors for the treatment of Diabetic Nephropathy

    Directory of Open Access Journals (Sweden)

    Gade Deepak Reddy

    2012-09-01

    Full Text Available Diabetic Nephropathy (DN is one of the major complications of diabetes mellitus, representing the leading of cause of chronic renal disease and a major cause of morbidity and mortality in both type 1 and type 2 diabetic patients. The Renin-Angiotensin-Aldosterone System (RAAS has been implicated in the pathophysiology of DN, and suggests a therapeutic target for blocking this system. Therefore, inhibition of RAAS plays a crucial role in the treatment of DN and therapeutic intervention mostly involves administration of angiotensin converting enzyme (ACE inhibitors and angiotensin AT1 receptor blockers. In this current study, we have used computational methods to design 37 novel ACE-inhibitors and evaluated them for the interaction with the enzyme ACE through insilico analysis. The obtained results were compared with the standard drug enalapril to find out the potential inhibitors. Here we report that ligand 4 exhibited strongest inhibitory activity among all. All the analogs are also screened for their ADME & Toxicity profiles using insilico tools and ligand 9 is having better binding affinity next to ligand 4, and also having better ADMET profile when compared to that of ligand 4. Post docking calculations were also performed for the docked complexes in order to identify the individual ligand binding energies by employing Multi-Ligand Bimolecular Association with Energetics (Embrace

  3. A New Determination of the Binding Energy of Atomic Oxygen on Dust Grain Surfaces: Experimental Results and Simulations

    CERN Document Server

    He, Jiao; Hopkins, Tyler; Vidali, Gianfranco; Kaufman, Michael J

    2015-01-01

    The energy to desorb atomic oxygen from an interstellar dust grain surface, $E_{\\rm des}$, is an important controlling parameter in gas-grain models; its value impacts the temperature range over which oxygen resides on a dust grain. However, no prior measurement has been done of the desorption energy. We report the first direct measurement of $E_{\\rm des}$ for atomic oxygen from dust grain analogs. The values of $E_{\\rm des}$ are $1660\\pm 60$~K and $1850\\pm 90$~K for porous amorphous water ice and for a bare amorphous silicate film, respectively, or about twice the value previously adopted in simulations of the chemical evolution of a cloud. We use the new values to study oxygen chemistry as a function of depth in a molecular cloud. For $n=10^4$ cm$^{-3}$ and $G_0$=10$^2$ ($G_0$=1 is the average local interstellar radiation field), the main result of the adoption of the higher oxygen binding energy is that H$_2$O can form on grains at lower visual extinction $A_{\\rm V}$, closer to the cloud surface. A higher ...

  4. Binding energies of shallow impurities in asymmetric strained wurtzite AlxGa1-xN/ GaN/Aly Ga1-yN quantum wells*

    Institute of Scientific and Technical Information of China (English)

    Ha Sihua; Ban Shiliang; Zhu Jun

    2011-01-01

    The ground state binding energies of hydrogenic impurities in strained wurtzite AlxGa1-xN/GaN/AlyGa1-yN quantum wells are calculated numerically by a variational method. The dependence of the binding energy on well width, impurity location and Al concentrations of the left and right barriers is discussed, including the effect of the built-in electric field induced by spontaneous and piezoelectric polarizations. The results show that the change in binding energy with well width is more sensitive to the impurity position and barrier heights than the barrier widths, especially in asymmetric well structures where the barrier widths and/or barrier heights differ. The binding energy as a function of the impurity position in symmetric and asymmetric structures behaves like a map of the spatial distribution of the ground state wave function of the electron. It is also found that the influence on the binding energy from the Al concentration of the left barrier is more obvious than that of the right barrier.

  5. Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method

    Science.gov (United States)

    Sugita, Masatake; Hirata, Fumio

    2016-09-01

    A protocol to calculate the binding free energy of a host-guest system is proposed based on the MM/3D-RISM method, taking cyclodextrin derivatives and their ligands as model systems. The protocol involves the procedure to identify the most probable binding mode (MPBM) of receptors and ligands by means of the umbrella sampling method. The binding free energies calculated by the MM/3D-RISM method for the complexes of the seven ligands with the MPBM of the cyclodextrin, and with the fluctuated structures around it, are in agreement with the corresponding experimental data in a semi-quantitative manner. It suggests that the protocol proposed here is promising for predicting the binding affinity of a small ligand to a relatively rigid receptor such as cyclodextrin.

  6. Effective nucleon mass, incompressibility, and third derivative of nuclear binding energy in the nonlinear relativistic mean field theory

    Energy Technology Data Exchange (ETDEWEB)

    Kouno, H.; Kakuta, N.; Noda, N.; Koide, K.; Mitsumori, T.; Hasegawa, A.; Nakano, M. (Department of Physics, Saga University, Saga 840 (Japan))

    1995-04-01

    We have studied the equations of state of nuclear matter using the nonlinear [sigma]-[omega] model. At the normal density, there is a strong correlation among the effective nucleon mass [ital M][sub 0][sup *], the incompressibility, [ital K] and the third derivative [ital K][prime] of binding energy. The results are compared with the empirical analysis of the giant isoscalar monopole resonances data. It is difficult to fit the data when [ital K][approx lt]200 MeV, using the model. It is also found that [ital K]=300[plus minus]50 MeV is favorable to account for the volume-symmetry properties of nuclear matter.

  7. MMPBSA decomposition of the binding energy throughout a molecular dynamics simulation of amyloid-beta (Abeta(10-35)) aggregation.

    Science.gov (United States)

    Campanera, Josep M; Pouplana, Ramon

    2010-04-15

    Recent experiments with amyloid-beta (Abeta) peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge of the structure of at the atomic level has not been achieved yet due to limitations of current experimental techniques. In this study, replica exchange molecular dynamics simulations are used to identify the expected diversity of dimer conformations of Abeta(10-35) monomers. The most representative dimer conformation has been used to track the dimer formation process between both monomers. The process has been characterized by means of the evolution of the decomposition of the binding free energy, which provides an energetic profile of the interaction. Dimers undergo a process of reorganization driven basically by inter-chain hydrophobic and hydrophilic interactions and also solvation/desolvation processes.

  8. MMPBSA Decomposition of the Binding Energy throughout a Molecular Dynamics Simulation of Amyloid-Beta (Aß10−35 Aggregation

    Directory of Open Access Journals (Sweden)

    Josep M. Campanera

    2010-04-01

    Full Text Available Recent experiments with amyloid-beta (Aβ peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer’s disease. The toxicity of Aβ oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge of the structure of at the atomic level has not been achieved yet due to limitations of current experimental techniques. In this study, replica exchange molecular dynamics simulations are used to identify the expected diversity of dimer conformations of Aβ10−35 monomers. The most representative dimer conformation has been used to track the dimer formation process between both monomers. The process has been characterized by means of the evolution of the decomposition of the binding free energy, which provides an energetic profile of the interaction. Dimers undergo a process of reorganization driven basically by inter-chain hydrophobic and hydrophilic interactions and also solvation/desolvation processes.

  9. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Juanjuan [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); Kara, Abdelkader, E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Department of Physics, University of Central Florida, Orlando, Florida 32816 (United States); Pasquali, Luca [Dipartimento di Ingegneria “E. Ferrari,” Università di Modena e Reggio Emilia, Via Vignolese 905, 41125 Modena (Italy); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy); Department of Physics, University of Johannesburg, P.O. Box 524, Auckland Park 2006 (South Africa); Bendounan, Azzedine; Sirotti, Fausto [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex (France); Esaulov, Vladimir A., E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy)

    2015-09-14

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.

  10. Virtual screening of mandelate racemase mutants with enhanced activity based on binding energy in the transition state.

    Science.gov (United States)

    Gu, Jiali; Liu, Min; Guo, Fei; Xie, Wenping; Lu, Wenqiang; Ye, Lidan; Chen, Zhirong; Yuan, Shenfeng; Yu, Hongwei

    2014-02-05

    Mandelate racemase (MR) is a promising candidate for the dynamic kinetic resolution of racemates. However, the poor activity of MR towards most of its non-natural substrates limits its widespread application. In this work, a virtual screening method based on the binding energy in the transition state was established to assist in the screening of MR mutants with enhanced catalytic efficiency. Using R-3-chloromandelic acid as a model substrate, a total of 53 mutants were constructed based on rational design in the two rounds of screening. The number of mutants for experimental validation was brought down to 17 by the virtual screening method, among which 14 variants turned out to possess improved catalytic efficiency. The variant V26I/Y54V showed 5.2-fold higher catalytic efficiency (k(cat)/K(m)) towards R-3-chloromandelic acid than that observed for the wild-type enzyme. Using this strategy, mutants were successfully obtained for two other substrates, R-mandelamide and R-2-naphthylglycolate (V26I and V29L, respectively), both with a 2-fold improvement in catalytic efficiency. These results demonstrated that this method could effectively predict the trend of mutational effects on catalysis. Analysis from the energetic and structural assays indicated that the enhanced interactions between the active sites and the substrate in the transition state led to improved catalytic efficiency. It was concluded that this virtual screening method based on the binding energy in the transition state was beneficial in enzyme rational redesign and helped to better understand the catalytic properties of the enzyme.

  11. Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.

    Science.gov (United States)

    Jayaram, B; McConnell, K; Dixit, S B; Das, A; Beveridge, D L

    2002-01-15

    Noncovalent association of proteins to specific target sites on DNA--a process central to gene expression and regulation--has thus far proven to be idiosyncratic and elusive to generalizations on the nature of the driving forces. The spate of structural information on protein--DNA complexes sets the stage for theoretical investigations on the molecular thermodynamics of binding aimed at identifying forces responsible for specific macromolecular recognition. Computation of absolute binding free energies for systems of this complexity transiting from structural information is a stupendous task. Adopting some recent progresses in treating atomic level interactions in proteins and nucleic acids including solvent and salt effects, we have put together an energy component methodology cast in a phenomenological mode and amenable to systematic improvements and developed a computational first atlas of the free energy contributors to binding in approximately 40 protein-DNA complexes representing a variety of structural motifs and functions. Illustrating vividly the compensatory nature of the free energy components contributing to the energetics of recognition for attaining optimal binding, our results highlight unambiguously the roles played by packing, electrostatics including hydrogen bonds, ion and water release (cavitation) in protein-DNA binding. Cavitation and van der Waals contributions without exception favor complexation. The electrostatics is marginally unfavorable in a consensus view. Basic residues on the protein contribute favorably to binding despite the desolvation expense. The electrostatics arising from the acidic and neutral residues proves unfavorable to binding. An enveloping mode of binding to short stretches of DNA makes for a strong unfavorable net electrostatics but a highly favorable van der Waals and cavitation contribution. Thus, noncovalent protein-DNA association is a system-specific fine balancing act of these diverse competing forces. With the

  12. Diels-Alder addition of some 6-and 5-member ring aromatic compounds on the Si(001)-2×1 surface: dependence of the binding energy on the resonance energy of the aromatic compounds

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An energy decomposition scheme is proposed for understanding of the relative lowbinding energy of the [4+2] cycloaddition of benzene on the Si(001)-2×1 surface. By means ofdensity functional cluster model calculations, this scheme is demonstrated to be applicable tosome other 6-and 5-member ring aromatic compounds, giving a trend that the binding energy ofthe [4+2] cycloaddition products of those aromatic compounds on the Si(001) surface dependsstrongly on their resonance energy.

  13. The Binding Energy, Spin-Excitation Gap, and Charged Gap in the Boson-Fermion Model

    Institute of Scientific and Technical Information of China (English)

    YANG Kai-Hua; TIAN Guang-Shan; HAN Ru-Qi

    2003-01-01

    In this paper, by applying a simplified version of Lieb 's spin-refleetion-positivity method, which was recentlydeveloped by one of us [G.S. Tian and J.G. Wang, J. Phys. A: Math. Gen. 35 (2002) 941], we investigate some generalproperties of the boson-fermion Hamiltonian, which has been widely used as a phenomenological model to describe thereal-space pairing of electrons. On a mathematically rigorous basis, we prove that for either negative or positive couplingV, which represents the spontaneous decay and recombination process between boson and fermion in the model, thepairing energy of electrons is nonzero. Furthermore, we also show that the spin-excitation gap of the boson-fermionHamiltonian is always larger than its charged gap, as predicted by the pre-paired electron theory.

  14. The Binding Energy, Spin-Excitation Gap, and Charged Gap in the Boson-Fermion Model

    Institute of Scientific and Technical Information of China (English)

    YANGKai-Hua; Guang-Shan; HANRu-Qi

    2003-01-01

    In this paper, by applying a simplified version of Lieb's spin-reflection-positivity method, which was recently developed by one of us [G.S. Tian and J.G. Wang, J. Phys. A: Math. Gen. 35 (2002) 941], we investigate some general properties of the boeon-fermion Hamiltonlan, which has been widely used as a phenomenological model to describe the real-space pairing of electrons. On a mathematically rigorous basis, we prove that for either negative or positive couping V, which represents the spontaneous decay and recombination process between boson and fermion in the model, the pairing energy of electrons is nonzero. Furthermore, we also show that the spin-excitation gap of the boson-fermion Hamiltonian is always larger than its charged gap, as predicted by the pre-palred electron theory.

  15. Core-level binding-energy shifts due to end effects in polymers: A Hartree-Fock Green's-function study

    Science.gov (United States)

    Seel, M.; Ladik, J.

    1985-10-01

    Hartree-Fock Green's-function studies of end effects on the core-level structure of metallic and insulating quasi-one-dimensional model polymers reveal additional core peaks outside the bulk bands. In the metallic case, shifts to both lower (~-150 meV) and higher (~+50 meV) binding energies are observed, whereas in the insulating case, split-off peaks occur only at the lower-binding-energy side (~-150 meV). It is shown that a positive or negative net valence population alone does not determine the direction of the shift. The binding-energy changes are determined by a detailed balance between the energy loss due to a decrease in the electron-nuclear attraction and the energy gain due to a decrease in the electron-electron repulsion experienced by the core electrons of the end atoms. This can probably also explain why for some metal surfaces, shifts towards lower, and for others, shifts towards higher, binding energies are found. In the valence region of the investigated lithium chains, the ends do not produce localized end states.

  16. A self-interaction-free local hybrid functional: Accurate binding energies vis-\\`a-vis accurate ionization potentials from Kohn-Sham eigenvalues

    CERN Document Server

    Schmidt, Tobias; Makmal, Adi; Kronik, Leeor; Kümmel, Stephan

    2014-01-01

    We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potent...

  17. Photoexcited triplet state provides a quantitative measure of intercalating drug-DNA binding energies

    Science.gov (United States)

    Maki, August H.; Alfredson, T. V.; Waring, M. J.

    1992-04-01

    A linear correlation between spectroscopic and thermodynamic properties of systems is rarely encountered. In triplet state ODMR studies of various DNA complexes of echinomycin, a quinoxaline-containing cyclic depsipeptide bis-intercalating antibiotic, and its biosynthesized quinoline analogs, such correlations are observed. The zero field splitting D-parameter of the intercalated quinoxaline or quinoline residue varies linearly with the free energy of drug-DNA complexing. From previous work, the DNA sequence specificity of echinomycin analogs is known to be influenced by the identity of the intercalating residue (e.g., quinoxaline vs. quinoline). The present results strongly suggest that the DNA sequence-specificity of these drugs is controlled largely by the intercalated residue, and that the energetics of the peptide- DNA interaction, although considerable, are relatively sequence independent. These conclusions run counter to the generally accepted idea that DNA recognition by sequence- seeking proteins is controlled by specific hydrogen bonding interactions. The high degree of N-methylation of the echinomycin peptide portion severely restricts these interactions, however. A simple theoretical model is presented to support the experimentally observed linear correlation between (Delta) D and (Delta) G.

  18. Energy-dependent reduced drug binding as a mechanism of Vinca alkaloid resistance in human leukemic lymphoblasts.

    Science.gov (United States)

    Beck, W T; Cirtain, M C; Lefko, J L

    1983-11-01

    ) was required only for subsequent release of what appeared to be a more tightly bound cell-associated fraction of VLB. Results of zero-time binding studies tended to confirm that VLB binding by resistant cells has two components, one requiring and the other not requiring metabolic energy. Differences in the proportions of these two components between the sensitive and resistant cells suggest a mechanism for resistance to VLB and similar compounds.

  19. Study on binding and fluorescence energy transfer efficiency of Rhodamine B with Pluronic F127-gold nanohybrid using optical spectroscopy methods

    Science.gov (United States)

    Antonisamy, Jenif Dsouza; Swain, Jitendriya; Dash, Sasmita

    2017-02-01

    This work focuses on the binding efficiency and fluorescence resonance energy transfer (FRET) of fluorescent dye Rhodamine B (Rh B) to Pluronic F127-gold nanohybrid. The formation of gold nanoparticles inside Rh B doped Pluronic F127 copolymer have been characterized using dynamic light scattering study, HR-TEM images, UV-visible spectra and fluorescence studies. Fluorescence quenching and the constant fluorescence lifetime of the Rhodamine B present in the cavity of Pluronic F127-gold nanohybrid suggested a strong binding ability (3.5 × 103 L mol- 1), static nature of quenching and better energy transfer efficiency of fluorescent dye towards Pluronic F127-gold (Au) nanohybrids.

  20. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

    Science.gov (United States)

    Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

    2016-09-01

    We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

  1. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

    Science.gov (United States)

    Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

    2016-09-01

    We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

  2. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

    Science.gov (United States)

    Yin, Jian; Henriksen, Niel M.; Slochower, David R.; Gilson, Michael K.

    2017-01-01

    The absolute binding free energies and binding enthalpies of twelve host-guest systems in the SAMPL5 blind challenge were computed using our attach-pull-release (APR) approach. This method has previously shown good correlations between experimental and calculated binding data in retrospective studies of cucurbit[7]uril (CB7) and β-cyclodextrin (βCD) systems. In the present work, the computed binding free energies for host octa acid (OA or OAH) and tetra-endo-methyl octa-acid (TEMOA or OAMe) with guests are in good agreement with prospective experimental data, with a coefficient of determination (R2) of 0.8 and root-mean-squared error of 1.7 kcal/mol using the TIP3P water model. The binding enthalpy calculations achieve moderate correlations, with R2 of 0.5 and RMSE of 2.5 kcal/mol, for TIP3P water. Calculations using the newly developed OPC water model also show good performance. Furthermore, the present calculations semi-quantitatively capture the experimental trend of enthalpy-entropy compensation observed, and successfully predict guests with the strongest and weakest binding affinity. The most populated binding poses of all twelve systems, based on clustering analysis of 750 ns molecular dynamics (MD) trajectories, were extracted and analyzed. Computational methods using MD simulations and explicit solvent models in a rigorous statistical thermodynamic framework, like APR, can generate reasonable predictions of binding thermodynamics. Especially with continuing improvement in simulation force fields, such methods hold the promise of making substantial contributions to hit identification and lead optimization in the drug discovery process.

  3. Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.

    Directory of Open Access Journals (Sweden)

    Yuzhen Niu

    Full Text Available As a promising target for the treatment of lung cancer, the MutT Homolog 1 (MTH1 protein can be inhibited by crizotinib. A recent work shows that the inhibitory potency of (S-crizotinib against MTH1 is about 20 times over that of (R-crizotinib. But the detailed molecular mechanism remains unclear. In this study, molecular dynamics (MD simulations and free energy calculations were used to elucidate the mechanism about the effect of chirality of crizotinib on the inhibitory activity against MTH1. The binding free energy of (S-crizotinib predicted by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA and Adaptive biasing force (ABF methodologies is much lower than that of (R-crizotinib, which is consistent with the experimental data. The analysis of the individual energy terms suggests that the van der Waals interactions are important for distinguishing the binding of (S-crizotinib and (R-crizotinib. The binding free energy decomposition analysis illustrated that residues Tyr7, Phe27, Phe72 and Trp117 were important for the selective binding of (S-crizotinib to MTH1. The adaptive biasing force (ABF method was further employed to elucidate the unbinding process of (S-crizotinib and (R-crizotinib from the binding pocket of MTH1. ABF simulation results suggest that the reaction coordinates of the (S-crizotinib from the binding pocket is different from (R-crizotinib. The results from our study can reveal the details about the effect of chirality on the inhibition activity of crizotinib to MTH1 and provide valuable information for the design of more potent inhibitors.

  4. Binding Energy of Ionized-Donor-Bound Excitons in the GaAs-AlxGa1-xAs Quantum Wells

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-Jun; ZHANG Shu-Fang; KONG Xiao-Jun; LI Shu-Shen

    2000-01-01

    The binding energy of an exciton bound to anionized donor impurity (D+, X) located at the center or the edgein GaAs-AlxGa1-xAs quantum wells is calculated variationally for the well width from 10 to 300 A by using atwo-parameter wave function, The theoretical results are discussed and compared with the previous experimentalresults.

  5. Tuning the Exciton Binding Energies in Single Self-Assembled InGaAs/GaAs Quantum Dots by Piezoelectric-Induced Biaxial Stress

    NARCIS (Netherlands)

    Ding, F.; Singh, R.; Plumhof, J.D.; Zander, T.; Křápek, V.; Chen, Y.H.; Benyoucef, M.; Zwiller, V.; Dörr, K.; Bester, G.; Rastelli, A.; Schmidt, O.G.

    2010-01-01

    We study the effect of an external biaxial stress on the light emission of single InGaAs/GaAs(001) quantum dots placed onto piezoelectric actuators. With increasing compression, the emission blueshifts and the binding energies of the positive trion (X+) and biexciton (XX) relative to the neutral exc

  6. Febrifugine analogues as Leishmania donovani trypanothione reductase inhibitors: binding energy analysis assisted by molecular docking, ADMET and molecular dynamics simulation.

    Science.gov (United States)

    Pandey, Rajan Kumar; Kumbhar, Bajarang Vasant; Srivastava, Shubham; Malik, Ruchi; Sundar, Shyam; Kunwar, Ambarish; Prajapati, Vijay Kumar

    2017-01-01

    Visceral leishmaniasis affects people from 70 countries worldwide, mostly from Indian, African and south American continent. The increasing resistance to antimonial, miltefosine and frequent toxicity of amphotericin B drives an urgent need to develop an antileishmanial drug with excellent efficacy and safety profile. In this study we have docked series of febrifugine analogues (n = 8813) against trypanothione reductase in three sequential docking modes. Extra precision docking resulted into 108 ligands showing better docking score as compared to two reference ligand. Furthermore, 108 febrifugine analogues and reference inhibitor clomipramine were subjected to ADMET, QikProp and molecular mechanics, the generalized born model and solvent accessibility study to ensure the toxicity caused by compounds and binding-free energy, respectively. Two best ligands (FFG7 and FFG2) qualifying above screening parameters were further subjected to molecular dynamics simulation. Conducting these studies, here we confirmed that 6-chloro-3-[3-(3-hydroxy-2-piperidyl)-2-oxo-propyl]-7-(4-pyridyl) quinazolin-4-one can be potential drug candidate to fight against Leishmania donovani parasites.

  7. Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants.

    Science.gov (United States)

    Feenstra, K Anton; Starikov, Eugene B; Urlacher, Vlada B; Commandeur, Jan N M; Vermeulen, Nico P E

    2007-03-01

    Hydroxylations of octane and lauric acid by Cytochrome P450-BM3 (CYP102A1) wild-type and three active site mutants--F87A, L188Q/A74G, and F87V/L188Q/A74G--were rationalized using a combination of substrate orientation from docking, substrate binding statistics from molecular dynamics simulations, and barrier energies for hydrogen atom abstraction from quantum mechanical calculations. Wild-type BM3 typically hydroxylates medium- to long-chain fatty acids on subterminal (omega-1, omega-2, omega-3) but not the terminal (omega) positions. The known carboxylic anchoring site Y51/R47 for lauric acid, and hydrophobic interactions and steric exclusion, mainly by F87, for octane as well as lauric acid, play a role in the binding modes of the substrates. Electrostatic interactions between the protein and the substrate strongly modulate the substrate's regiodependent activation barriers. A combination of the binding statistics and the activation barriers of hydrogen-atom abstraction in the substrates is proposed to determine the product formation. Trends observed in experimental product formation for octane and lauric acid by wild-type BM3 and the three active site mutants were qualitatively explained. It is concluded that the combination of substrate binding statistics and hydrogen-atom abstraction barrier energies is a valuable tool to rationalize substrate binding and product formation and constitutes an important step toward prediction of product ratios.

  8. Effects of an Intense Laser Field and Hydrostatic Pressure on the Intersubband Transitions and Binding Energy of Shallow Donor Impurities in a Quantum Well

    Institute of Scientific and Technical Information of China (English)

    U. Yesilgul; F. Ungan; E. Kasapoglu; H. Sari; I. S(o)kmen

    2011-01-01

    We have calculated the intersubband transitions and the ground-state binding energies of a hydrogenic donor impurity in a quantum well in the presence of a high-frequency laser field and hydrostatic pressure.The calculations are performed within the effective mass approximation,using a variational method. We conclude that the laser field amplitude and the hydrostatic pressure provide an important effect on the electronic and optical properties of the quantum wells.According to the results obtained from the present work,it is deduced that (i) the binding energies of donor impurity decrease as the laser field increase,(ii) the binding energies of donor impurity increase as the hydrostatic pressure increase,(iii) the intersubband absorption coefficients shift toward lower energies as the hydrostatic pressure increases,(iv) the magnitude of absorption coefficients decrease and also shift toward higher energies as the laser field increase.It is hopeful that the obtained results will provide important improvements in device applications.

  9. Control of the binding energy by tuning the single dopant position, magnetic field strength and shell thickness in ZnS/CdSe core/shell quantum dot

    Science.gov (United States)

    Talbi, A.; Feddi, E.; Zouitine, A.; Haouari, M. El; Zazoui, M.; Oukerroum, A.; Dujardin, F.; Assaid, E.; Addou, M.

    2016-10-01

    Recently, the new tunable optoelectronic devices associated to the inclusion of the single dopant are in continuous emergence. Combined to other effects such as magnetic field, geometrical confinement and dielectric discontinuity, it can constitute an approach to adjusting new transitions. In this paper, we present a theoretical investigation of magnetic field, donor position and quantum confinement effects on the ground state binding energy of single dopant confined in ZnS/CdSe core/shell quantum dot. Within the framework of the effective mass approximation, the Schrödinger equation was numerically been solved by using the Ritz variational method under the finite potential barrier. The results show that the binding energy is very affected by the core/shell sizes and by the external magnetic field. It has been shown that the single dopant energy transitions can be controlled by tuning the dopant position and/or the field strength.

  10. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

    Science.gov (United States)

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

    2015-01-22

    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

  11. Characteristics of DNA-binding proteins determine the biological sensitivity to high-linear energy transfer radiation

    NARCIS (Netherlands)

    H. Wang (Hong); X. Zhang (Xiangming); P. Wang (Ping); X. Yu (Xiaoyan); J. Essers (Jeroen); D.J. Chen (David); R. Kanaar (Roland); S. Takeda (Shiunichi); Y. Wang (Ya)

    2010-01-01

    textabstractNon-homologous end-joining (NHEJ) and homologous recombination repair (HRR), contribute to repair ionizing radiation (IR)-induced DNA double-strand breaks (DSBs). Mre11 binding to DNA is the first step for activating HRR and Ku binding to DNA is the first step for initiating NHEJ. High-l

  12. Absolute Free Energy of Binding and Entropy of the FKBP12-FK506 Complex: Effects of the Force Field.

    Science.gov (United States)

    General, Ignacio J; Meirovitch, Hagai

    2013-10-08

    The hypothetical scanning molecular dynamics (HSMD) method combined with thermodynamic integration (HSMD-TI) has been extended recently for calculating ΔA(0)-the absolute free energy of binding of a ligand to a protein. With HSMD-TI, ΔA(0) is obtained in a new way as a sum of several components, among them is ΔSligand-the change in the conformational entropy as the ligand is transferred from the bulk solvent to the active site-this entropy is obtained by a specific reconstruction procedure. This unique aspect of HSMD (which is useful in rational drug design) is in particular important for treating large ligands, where ΔSligand might be significant. Technically, one should verify that the results for ΔSligand converge-a property that might become more difficult for large ligands; therefore, studying ligands of increasing size would define the range of applicability of HSMD-TI for binding. In this paper, we check the performance of HSMD-TI by applying it to the relatively large ligand FK506 (126 atoms) complexed with the protein FKBP12, where ΔA(0) = -12.8 kcal/mol is known experimentally as well as the crystal structure of the complex. This structure was initially equilibrated by carrying out a 100 ns molecular dynamics trajectory, where the system is modeled by the AMBER force field, TIP3P water, and Particle Mesh Ewald. HSMD-TI calculations were carried out in three conformational regions defined by the intervals [0.2,2], [2,5], and [5,100] ns along the trajectory, where local equilibration of the total energy has been observed; we obtained ΔA(0) = -13.6 ± 1.1, -16.6 ± 1.4, and -16.7 ± 1.4 kcal/mol, respectively indicating the following: (1) The second and third regions belong to the same conformational subspace of the complex, which is different from the [0.2,2] ns subspace. (2) The unsatisfactory result for ΔA(0) obtained in the well equilibrated (hence theoretically preferred) latter regions reflects the nonperfect modeling used, which however (3

  13. Thickness-Dependent Binding Energy Shift in Few-Layer MoS2 Grown by Chemical Vapor Deposition.

    Science.gov (United States)

    Lin, Yu-Kai; Chen, Ruei-San; Chou, Tsu-Chin; Lee, Yi-Hsin; Chen, Yang-Fang; Chen, Kuei-Hsien; Chen, Li-Chyong

    2016-08-31

    The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts.

  14. Linear free energy relationships for metal-ligand complexation: Bidentate binding to negatively-charged oxygen donor atoms

    Science.gov (United States)

    Carbonaro, Richard F.; Atalay, Yasemin B.; Di Toro, Dominic M.

    2011-05-01

    Stability constants for metal complexation to bidentate ligands containing negatively-charged oxygen donor atoms can be estimated from the following linear free energy relationship (LFER): log KML = χOO( αO log KHL,1 + αO log KHL,2) where KML is the metal-ligand stability constant for a 1:1 complex, KHL,1 and KHL,2 are the proton-ligand stability constants (the ligand p Ka values), and αO is the Irving-Rossotti slope. The parameter χOO is metal specific and has slightly different values for five and six membered chelate rings. LFERs are presented for 21 different metal ions and are accurate to within approximately 0.30 log units in predictions of log KML values. Ligands selected for use in LFER development include dicarboxylic acids, carboxyphenols, and ortho-diphenols. For ortho-hydroxybenzaldehydes, α-hydroxycarboxylic acids, and α-ketocarboxylic acids, a modification of the LFER where log KHL,2 is set equal to zero is required. The chemical interpretation of χOO is that it accounts for the extra stability afforded to metal complexes by the chelate effect. Cu-NOM binding constants calculated from the bidentate LFERs are similar in magnitude to those used in WHAM 6. This LFER can be used to make log KML predictions for small organic molecules. Since natural organic matter (NOM) contains many of the same functional groups (i.e. carboxylic acids, phenols, alcohols), the LFER log KML predictions shed light on the range of appropriate values for use in modeling metal partitioning in natural systems.

  15. Observation of core-level binding energy shifts between (100) surface and bulk atoms of epitaxial CuInSe{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, A.J. [Colorado School of Mines, Golden, CO (United States); Berry, G.; Rockett, A. [Univ. of Illinois, Urbana-Champaign, IL (United States)] [and others

    1997-04-01

    Core-level and valence band photoemission from semiconductors has been shown to exhibit binding energy differences between surface atoms and bulk atoms, thus allowing one to unambiguously distinguish between the two atomic positions. Quite clearly, surface atoms experience a potential different from the bulk due to the lower coordination number - a characteristic feature of any surface is the incomplete atomic coordination. Theoretical accounts of this phenomena are well documented in the literature for III-V and II-VI semiconductors. However, surface state energies corresponding to the equilibrium geometry of (100) and (111) surfaces of Cu-based ternary chalcopyrite semiconductors have not been calculated or experimental determined. These compounds are generating great interest for optoelectronic and photovoltaic applications, and are an isoelectronic analog of the II-VI binary compound semiconductors. Surface core-level binding energy shifts depend on the surface cohesive energies, and surface cohesive energies are related to surface structure. For ternary compound semiconductor surfaces, such as CuInSe{sub 2}, one has the possibility of variations in surface stoichiometry. Applying standard thermodynamical calculations which consider the number of individual surface atoms and their respective chemical potentials should allow one to qualitatively determine the magnitude of surface core-level shifts and, consequently, surface state energies.

  16. The electronic structure and grain boundary segregation by boron addition——A binding energy shifting criterion for the brittle-ductile fracture transition in Ni3Al

    Institute of Scientific and Technical Information of China (English)

    张云; 林栋梁

    1997-01-01

    The electronic structure and grain boundary segregation caused by boron addition to Ni3Al have been studied by X-ray photoelectron spectroscopy and Auger electron spectroscopy, respectively. The obtained results show that the Ni2p3/2 electron binding energy rises gradually in the sequence of pure Ni< Ni76Al24< Ni74Al26 < Ni25Al25, while it reduces monotonously with an increase in boron addition to Ni3Al. Besides, it is found that the gram boundary segregation of boron occurring in Ni3Al is a combined equilibrium and non-equilibrium type in nature. Based on the concept of the bonding environmental inhomogeneity, measured by the shift in Ni2p3/2 electron binding energy from the nickel atoms in the simple substance nickel to those in the intermetallic compound Ni3Al (ΔEB), being responsible for the brittle behavior of the alloy, a binding energy shifting criterion for the brittle-ductile fracture transition in Ni3Al is presented: when ΔEB>0, the brittle failure occurs in Ni3Al; when ΔEB<0, the ductile o

  17. Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design.

    Science.gov (United States)

    You, Wanli; Huang, Yu-Ming M; Kizhake, Smitha; Natarajan, Amarnath; Chang, Chia-En A

    2016-08-01

    Inhibition of the protein-protein interaction (PPI) mediated by breast-cancer-gene 1 C-terminal (BRCT) is an attractive strategy to sensitize breast and ovarian cancers to chemotherapeutic agents that induce DNA damage. Such inhibitors could also be used for studies to understand the role of this PPI in DNA damage response. However, design of BRCT inhibitors is challenging because of the inherent flexibility associated with this domain. Several studies identified short phosphopeptides as tight BRCT binders. Here we investigated the thermodynamic properties of 18 phosphopeptides or peptide with phosphate mimic and three compounds with phosphate groups binding to BRCT to understand promiscuous molecular recognition and guide inhibitor design. We performed molecular dynamics (MD) simulations to investigate the interactions between inhibitors and BRCT and their dynamic behavior in the free and bound states. MD simulations revealed the key role of loops in altering the shape and size of the binding site to fit various ligands. The mining minima (M2) method was used for calculating binding free energy to explore the driving forces and the fine balance between configuration entropy loss and enthalpy gain. We designed a rigidified ligand, which showed unfavorable experimental binding affinity due to weakened enthalpy. This was because it lacked the ability to rearrange itself upon binding. Investigation of another phosphate group containing compound, C1, suggested that the entropy loss can be reduced by preventing significant narrowing of the energy well and introducing multiple new compound conformations in the bound states. From our computations, we designed an analog of C1 that introduced new intermolecular interactions to strengthen attractions while maintaining small entropic penalty. This study shows that flexible compounds do not always encounter larger entropy penalty, compared with other more rigid binders, and highlights a new strategy for inhibitor design.

  18. Investigations on Binding Pattern of Kinase Inhibitors with PPARγ: Molecular Docking, Molecular Dynamic Simulations, and Free Energy Calculation Studies

    Science.gov (United States)

    Mazumder, Mohit; Das, Umashankar; Gourinath, Samudrala

    2017-01-01

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential target for the treatment of several disorders. In view of several FDA approved kinase inhibitors, in the current study, we have investigated the interaction of selected kinase inhibitors with PPARγ using computational modeling, docking, and molecular dynamics simulations (MDS). The docked conformations and MDS studies suggest that the selected KIs interact with PPARγ in the ligand binding domain (LBD) with high positive predictive values. Hence, we have for the first time shown the plausible binding of KIs in the PPARγ ligand binding site. The results obtained from these in silico investigations warrant further evaluation of kinase inhibitors as PPARγ ligands in vitro and in vivo.

  19. First-principles investigation on the electronic efficiency and binding energy of the contacts formed by graphene and poly-aromatic hydrocarbon anchoring groups

    KAUST Repository

    Li, Yang

    2015-04-28

    © 2015 AIP Publishing LLC. The electronic efficiency and binding energy of contacts formed between graphene electrodes and poly-aromatic hydrocarbon (PAH) anchoring groups have been investigated by the non-equilibrium Green\\'s function formalism combined with density functional theory. Our calculations show that PAH molecules always bind in the interior and at the edge of graphene in the AB stacking manner, and that the binding energy increases following the increase of the number of carbon and hydrogen atoms constituting the PAH molecule. When we move to analyzing the electronic transport properties of molecular junctions with a six-carbon alkyne chain as the central molecule, the electronic efficiency of the graphene-PAH contacts is found to depend on the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the corresponding PAH anchoring group, rather than its size. To be specific, the smaller is the HOMO-LUMO gap of the PAH anchoring group, the higher is the electronic efficiency of the graphene-PAH contact. Although the HOMO-LUMO gap of a PAH molecule depends on its specific configuration, PAH molecules with similar atomic structures show a decreasing trend for their HOMO-LUMO gap as the number of fused benzene rings increases. Therefore, graphene-conjugated molecule-graphene junctions with high-binding and high-conducting graphene-PAH contacts can be realized by choosing appropriate PAH anchor groups with a large area and a small HOMO-LUMO gap.

  20. On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge

    Science.gov (United States)

    Bansal, Nupur; Zheng, Zheng; Cerutti, David S.; Merz, Kenneth M.

    2017-01-01

    We review our performance in the SAMPL5 challenge for predicting host-guest binding affinities using the movable type (MT) method. The challenge included three hosts, acyclic Cucurbit[2]uril and two octa-acids with and without methylation at the entrance to their binding cavities. Each host was associated with 6-10 guest molecules. The MT method extrapolates local energy landscapes around particular molecular states and estimates the free energy by Monte Carlo integration over these landscapes. Two blind submissions pairing MT with variants of the KECSA potential function yielded mean unsigned errors of 1.26 and 1.53 kcal/mol for the non-methylated octa-acid, 2.83 and 3.06 kcal/mol for the methylated octa-acid, and 2.77 and 3.36 kcal/mol for Cucurbit[2]uril host. While our results are in reasonable agreement with experiment, we focused on particular cases in which our estimates gave incorrect results, particularly with regard to association between the octa-acids and an adamantane derivative. Working on the hypothesis that differential solvation effects play a role in effecting computed binding affinities for the parent octa-acid and the methylated octa-acid and that the ligands bind inside the pockets (rather than on the surface) we devised a new solvent accessible surface area term to better quantify solvation energy contributions in MT based studies. To further explore this issue a, molecular dynamics potential of mean force (PMF) study indicates that, as found by our docking calculations, the stable binding mode for this ligand is inside (rather than surface bound) the octa-acid cavity whether the entrance is methylated or not. The PMF studies also obtained the correct order for the methylation-induced change in binding affinities and associated the difference, to a large extent to differential solvation effects. Overall, the SAMPL5 challenge yielded in improvements our solvation modeling and also demonstrated the need for thorough validation of input data

  1. Structures, stabilization energies, and binding energies of quinoxaline···(H2O)(n), quinoxaline dimer, and quinoxaline···Cu complexes: a theoretical study.

    Science.gov (United States)

    Kabanda, Mwadham M; Ebenso, Eno E

    2013-02-21

    Quinoxaline is a parent structure for a broad class of N-heteroaromatic compounds, many of which exhibit various biological activities. The interaction of quinoxaline with explicit water molecules or metal ions and the formation of quinoxaline dimer play an important role in many of the biological activities of quinoxaline. This study investigates the structures, stabilization, and binding energies of quinoxaline complexes with water, transition metal ions, and quinoxaline dimer to provide information on the preferred geometries, interaction energies, and type of noncovalent interactions accounting for the stability of the complexes. The investigations are performed in vacuo and in water solution using MP2 and DFT methods. The results of the study on the quinoxaline···(H(2)O)(n) show that the preferred adducts in vacuo involve one, two, or three water molecules hydrogen bonded to the N atom and the neighboring H atom of the C(sp2)-H group. The results in water solution show a preference for water-water clustering. The dimers of quinoxaline are stabilized by either π-π stacking or weak C-H···N intermolecular hydrogen bonds. The relative stability of the quinoxaline···Cu complexes depends on the site on which the Cu ion binds and the binding strength depends on both the nature of the cation and the binding site.

  2. Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    DiLabio, Gino A., E-mail: Gino.DiLabio@nrc.ca [National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9 (Canada); Department of Chemistry, University of British Columbia, Okanagan, 3333 University Way, Kelowna, British Columbia V1V 1V7 (Canada); Koleini, Mohammad [National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9 (Canada); Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4 (Canada)

    2014-05-14

    Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules. Specifically, the DCPs developed herein for the C, H, N, and O atoms provide binding energies for a set of 66 noncovalently bonded molecular dimers (the “S66” set) with a mean absolute error (MAE) of 0.21 kcal/mol, which represents an improvement of more than a factor of 10 over unadorned LC-ωPBE/6-31+G(2d,2p) and almost a factor of two improvement over LC-ωPBE/6-31+G(2d,2p) used in conjunction with the “D3” pairwise dispersion energy corrections. In addition, the DCPs reduce the MAE of calculated X-H and X-Y (X,Y = C, H, N, O) bond dissociation enthalpies for a set of 40 species from 3.2 kcal/mol obtained with unadorned LC-ωPBE/6-31+G(2d,2p) to 1.6 kcal/mol. Our findings demonstrate that broad improvements to the performance of DFT methods may be achievable through the use of DCPs.

  3. Dielectric confinement on exciton binding energy and nonlinear optical properties in a strained Zn1-xinMgxinSe/Zn1-xoutMgxoutSe quantum well

    Institute of Scientific and Technical Information of China (English)

    J. Abraham Hudson Mark; A. John Peter

    2012-01-01

    The band offsets for a Zn1-xinMgxin Se/Zn1-xoutMgxout Se quantum well heterostructure are determined using the model solid theory.The heavy hole exciton binding energies are investigated with various Mg alloy contents.The effect of mismatch between the dielectric constants between the well and the barrier is taken into account.The dependence of the excitonic transition energies on the geometrical confinement and the Mg alloy is discussed.Non-linear optical properties are determined using the compact density matrix approach.The linear,third order non-linear optical absorption coefficient values and the refractive index changes of the exciton are calculated for different concentrations of magnesium.The results show that the occurred blue shifts of the resonant peak due to the Mg incorporation give the information about the variation of two energy levels in the quantum well width.

  4. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T)

    Science.gov (United States)

    Caldararu, Octav; Olsson, Martin A.; Riplinger, Christoph; Neese, Frank; Ryde, Ulf

    2017-01-01

    We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO-CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by 50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11-16 kJ/mol. DLPNO-CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates

  5. Energy-resolved collision-induced dissociation studies of 1,10-phenanthroline complexes of the late first-row divalent transition metal cations: determination of the third sequential binding energies.

    Science.gov (United States)

    Nose, Holliness; Chen, Yu; Rodgers, M T

    2013-05-23

    The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated.

  6. Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface

    Science.gov (United States)

    Löytynoja, T.; Li, X.; Jänkälä, K.; Rinkevicius, Z.; Ågren, H.

    2016-07-01

    We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

  7. Experimental measurements of water molecule binding energies for the second and third solvation shells of [Ca(H2O)n]2+ complexes

    Science.gov (United States)

    Bruzzi, E.; Stace, A. J.

    2017-01-01

    Further understanding of the biological role of the Ca2+ ion in an aqueous environment requires quantitative measurements of both the short- and long-range interactions experienced by the ion in an aqueous medium. Here, we present experimental measurements of binding energies for water molecules occupying the second and, quite possibly, the third solvation shell surrounding a central Ca2+ ion in [Ca(H2O)n]2+ complexes. Results for these large, previously inaccessible, complexes have come from the application of finite heat bath theory to kinetic energy measurements following unimolecular decay. Even at n = 20, the results show water molecules to be more strongly bound to Ca2+ than would be expected just from the presence of an extended network of hydrogen bonds. For n > 10, there is very good agreement between the experimental binding energies and recently published density functional theory calculations. Comparisons are made with similar data recorded for [Ca(NH3)n]2+ and [Ca(CH3OH)n]2+ complexes.

  8. Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface.

    Science.gov (United States)

    Löytynoja, T; Li, X; Jänkälä, K; Rinkevicius, Z; Ågren, H

    2016-07-14

    We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

  9. On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer

    Science.gov (United States)

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2015-03-01

    We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for De = - 16.1 ± 0.1 kcal/mol and for D0 = - 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of -14.22 ± 0.12 kcal/mol.

  10. Extended x-ray--absorption fine structure of small Cu and Ni clusters: Binding-energy and bond-length changes with cluster size

    Energy Technology Data Exchange (ETDEWEB)

    Apai, G.; Hamilton, J.F.; Stohr, J.; Thompson, A.

    1979-07-09

    Extended x-ray--absorption fine-structure measurements have been made on metal clusters of Cu and Ni which were formed by vapor deposition on amorphous carbon substrates. Small clusters of both elements show a substantial contraction of the nearest-neighbor metal-metal distance and an increase in binding energy for the onset of the K absorption edge. The results are explained by the increasing surface-to-volume ratio as the cluster size decreases resulting in a more free-atom--like configuration of the metal atoms.

  11. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    Science.gov (United States)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  12. Bimodal intramolecular excitation energy transfer in a multichromophore photosynthetic model system: hybrid fusion proteins comprising natural phycobilin- and artificial chlorophyll-binding domains.

    Science.gov (United States)

    Zeng, Xiao-Li; Tang, Kun; Zhou, Nan; Zhou, Ming; Hou, Harvey J M; Scheer, Hugo; Zhao, Kai-Hong; Noy, Dror

    2013-09-11

    The phycobilisomes of cyanobacteria and red-algae are highly efficient peripheral light-harvesting complexes that capture and transfer light energy in a cascade of excitation energy transfer steps through multiple phycobilin chromophores to the chlorophylls of core photosystems. In this work, we focus on the last step of this process by constructing simple functional analogs of natural phycobilisome-photosystem complexes that are based on bichromophoric protein complexes comprising a phycobilin- and a chlorophyll- or porphyrin-binding domain. The former is based on ApcE(1-240), the N-terminal chromophore-binding domain of the phycobilisome's L(CM) core-membrane linker, and the latter on HP7, a de novo designed four-helix bundle protein that was originally planned as a high-affinity heme-binding protein, analogous to b-type cytochromes. We fused a modified HP7 protein sequence to ApcEΔ, a water-soluble fragment of ApcE(1-240) obtained by excising a putative hydrophobic loop sequence of residues 77-153. HP7 was fused either to the N- or the C-terminus of ApcEΔ or inserted between residues 76 and 78, thereby replacing the native hydrophobic loop domain. We describe the assembly, spectral characteristics, and intramolecular excitation energy transfer of two unique systems: in the first, the short-wavelength absorbing zinc-mesoporphyrin is bound to the HP7 domain and serves as an excitation-energy donor to the long-wavelength absorbing phycocyanobilin bound to the ApcE domain; in the second, the short-wavelength absorbing phycoerythrobilin is bound to the ApcE domain and serves as an excitation energy donor to the long-wavelength absorbing zinc-bacteriochlorophyllide bound to the HP7 domain. All the systems that were constructed and tested exhibited significant intramolecular fluorescence resonance energy transfer with yields ranging from 21% to 50%. This confirms that our modular, covalent approach for studying EET between the cyclic and open chain tetrapyrroles is

  13. Shining light on radiation detection and energy transfer : Triazole ligands used for detection of radiation and lanthanide binding

    NARCIS (Netherlands)

    Dijkstra, Peter

    2016-01-01

    Some substances, fluorophores, absorb light and then emit that light again as fluorescence. Apart from absorption of light, some of these substances can also emit light after having absorbed energy from radiation. A substance which can absorb radiation and emit the energy as light is called a scinti

  14. Nanoscale characteristics of triacylglycerol oils: phase separation and binding energies of two-component oils to crystalline nanoplatelets.

    Science.gov (United States)

    MacDougall, Colin J; Razul, M Shajahan; Papp-Szabo, Erzsebet; Peyronel, Fernanda; Hanna, Charles B; Marangoni, Alejandro G; Pink, David A

    2012-01-01

    Fats are elastoplastic materials with a defined yield stress and flow behavior and the plasticity of a fat is central to its functionality. This plasticity is given by a complex tribological interplay between a crystalline phase structured as crystalline nanoplatelets (CNPs) and nanoplatelet aggregates and the liquid oil phase. Oil can be trapped within microscopic pores within the fat crystal network by capillary action, but it is believed that a significant amount of oil can be trapped by adsorption onto crystalline surfaces. This, however, remains to be proven. Further, the structural basis for the solid-liquid interaction remains a mystery. In this work, we demonstrate that the triglyceride liquid structure plays a key role in oil binding and that this binding could potentially be modulated by judicious engineering of liquid triglyceride structure. The enhancement of oil binding is central to many current developments in this area since an improvement in the health characteristics of fat and fat-structured food products entails a reduction in the amount of crystalline triacylglycerols (TAGs) and a relative increase in the amount of liquid TAGs. Excessive amounts of unbound, free oil, will lead to losses in functionality of this important food component. Engineering fats for enhanced oil binding capacity is thus central to the design of more healthy food products. To begin to address this, we modelled the interaction of triacylglycerol oils, triolein (OOO), 1,2-olein elaidin (OOE) and 1,2-elaidin olein (EEO) with a model crystalline nanoplatelet composed of tristearin in an undefined polymorphic form. The surface of the CNP in contact with the oil was assumed to be planar. We considered pure OOO and mixtures of OOO + OOE and OOO + EEO with 80% OOO. The last two cases were taken as approximations to high oleic sunflower oil (HOSO). The intent was to investigate whether phase separation on a nanoscale took place. We defined an "oil binding capacity" parameter, B

  15. Benzene on Cu(111): I. Application of van der Waals-Density Functional Formalism to Determine Binding Sites and Energy Contour Map

    Science.gov (United States)

    Berland, Kristian; Einstein, T. L.; Hyldgaard, Per

    2010-03-01

    With a recently developed van der Waals density functional (vdW-DF)footnotetextM. Dion et al., Phys. Rev. Lett. 92 (2004) 246401 we study the adsorption of benzene on Cu(111).footnotetextKB, TLE, and PH, Phys. Rev. B 80 (2009) 155431 The vdW-DF inclusion of nonlocal correlations changes the relative stability of 8 high-symmetry binding-position options and increases the adsorption energy by over an order of magnitude, achieving good agreement with experiment. The metallic surface state survives benzene adsorption. From a contour plot of the potential energy, we find that benzene can move almost freely along a honeycomb web of ``corridors" linking fcc and hcp sites via bridge sites, consistent with the low diffusion barrier in experiment.

  16. Tight-binding branch-point energies and band offsets for cubic InN, GaN, AlN, and AlGaN alloys

    Science.gov (United States)

    Mourad, Daniel

    2013-03-01

    Starting with empirical tight-binding band structures, the branch-point (BP) energies and resulting valence band offsets for the zincblende phase of InN, GaN, and AlN are calculated from their k-averaged midgap energy. Furthermore, the directional dependence of the BPs of GaN and AlN is discussed using the Green's function method of Tersoff. We then show how to obtain the BPs for binary semiconductor alloys within a band-diagonal representation of the coherent potential approximation and apply this method to cubic AlGaN alloys. The resulting band offsets show good agreement to available experimental and theoretical data from the literature. Our results can be used to determine the band alignment in isovalent heterostructures involving pure cubic III-nitrides or AlGaN alloys for arbitrary concentrations.

  17. Formation and properties of astrophysical carbonaceous dust. I: ab-initio calculations of the configuration and binding energies of small carbon clusters

    CERN Document Server

    Mauney, Christopher; Lazzati, Davide

    2014-01-01

    The binding energies of n < 100 carbon clusters are calculated using the ab-initio density functional theory code Quantum Espresso. Carbon cluster geometries are determined using several levels of classical techniques and further refined using density functional theory. The resulting energies are used to compute the work of cluster formation and the nucleation rate in a saturated, hydrogen-poor carbon gas. Compared to classical calculations that adopt the capillary approximation, we find that nucleation of carbon clusters is enhanced at low temperatures and depressed at high temperatures. This difference is ascribed to the different behavior of the critical cluster size. We find that the critical cluster size is at n = 27 or n = 8 for a broad range of temperatures and saturations, instead of being a smooth function of such parameters. The results of our calculations can be used to follow carbonaceous cluster/grain formation, stability, and growth in hydrogen poor environments, such as the inner layers of c...

  18. Photoelectron spectroscopy of aqueous solutions: streaming potentials of NaX (X = Cl, Br, and I) solutions and electron binding energies of liquid water and X-.

    Science.gov (United States)

    Kurahashi, Naoya; Karashima, Shutaro; Tang, Ying; Horio, Takuya; Abulimiti, Bumaliya; Suzuki, Yoshi-Ichi; Ogi, Yoshihiro; Oura, Masaki; Suzuki, Toshinori

    2014-05-07

    The streaming potentials of liquid beams of aqueous NaCl, NaBr, and NaI solutions are measured using soft X-ray, He(I), and laser multiphoton ionization photoelectron spectroscopy. Gaseous molecules are ionized in the vicinity of liquid beams and the photoelectron energy shifts are measured as a function of the distance between the ionization point and the liquid beam. The streaming potentials change their polarity with concentration of electrolytes, from which the singular points of concentration eliminating the streaming potentials are determined. The streaming currents measured in air also vanish at these concentrations. The electron binding energies of liquid water and I(-), Br(-), and Cl(-) anions are revisited and determined more accurately than in previous studies.

  19. Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy calculations and descriptor analysis.

    Science.gov (United States)

    Tambunan, Usman Sumo Friend; Wulandari, Evi Kristin

    2010-10-15

    Human papillomaviruses (HPVs) are the most common on sexually transmitted viruses in the world. HPVs are responsible for a large spectrum of deseases, both benign and malignant. The certain types of HPV are involved in the development of cervical cancer. In attemps to find additional drugs in the treatment of cervical cancer, inhibitors of the histone deacetylases (HDAC) have received much attention due to their low cytotoxic profiles and the E6/E7 oncogene function of human papilomavirus can be completely by passed by HDAC inhibition. The histone deacetylase inhibitors can induce growth arrest, differentiation and apoptosis of cancer cells. HDAC class I and class II are considered the main targets for cancer. Therefore, the six HDACs class II was modeled and about two inhibitors (SAHA and TSA) were docked using AutoDock4.2, to each of the inhibitor in order to identify the pharmacological properties. Based on the results of docking, SAHA and TSA were able to bind with zinc ion in HDACs models as a drug target. SAHA was satisfied almost all the properties i.e., binding affinity, the Drug-Likeness value and Drug Score with 70% oral bioavailability and the carbonyl group of these compound fits well into the active site of the target where the zinc is present. Hence, SAHA could be developed as potential inhibitors of class II HDACs and valuable cervical cancer drug candidate.

  20. Semiphenomenological approximation of the sums of experimental radiative strength functions for dipole gamma transitions of energy E γ below the neutron binding energy B n for mass numbers in the range 40 ≤ A ≤ 200

    Science.gov (United States)

    Sukhovoj, A. M.; Furman, W. I.; Khitrov, V. A.

    2008-06-01

    The sums of radiative strength functions for primary dipole gamma transitions, k( E1) + k( M1), are approximated to a high precision by a superposition of two functional dependences in the energy range 0.5 125Te, 128I, 137,138,139Ba, 140La, 150Sm, 156,158Gd, 160Tb, 163,164,165Dy, 166Ho, 168Er, 170Tm, 174Yb, 176,177Lu, 181Hf, 182Ta, 183,184,185,187W, 188,190,191,193Os, 192Ir, 196Pt, 198Au, and 200Hg nuclei. It is shown that, in any nuclei, radiative strength functions are a dynamical quantity and that the values of k( E1) + k( M1) for specific energies of gamma transitions and specific nuclei are determined by the structure of decaying and excited levels, at least up to the neutron binding energy B n .

  1. Daily energy balance in growth hormone receptor/binding protein (GHR−/−) gene-disrupted mice is achieved through an increase in dark-phase energy efficiency

    Science.gov (United States)

    Longo, Kenneth A.; Berryman, Darlene E.; Kelder, Bruce; Charoenthongtrakul, Soratree; DiStefano, Peter S.; Geddes, Brad J.; Kopchick, John

    2009-01-01

    The goal of this study was to examine factors that contribute to energy balance in female GHR −/− mice. We measured energy intake, energy expenditure (EE), fuel utilization, body mass (Mb) changes and physical activity in 17 month-old female GHR −/− mice and their age-matched wild type littermates. The GHR −/− mice were smaller, consumed more food per unit Mb, had greater EE per unit Mb and had an increase in 24-h EE/Mb that was similar to the increase in their surface-area-to-volume ratio. Locomotor activity (LMA) was reduced in the GHR −/− mice, but the energetic cost associated with their LMA was greater than in wild type controls. Furthermore, Mb and LMA were independent explanatory covariates of most of the variance in EE, and when adjusted for Mb and LMA, the GHR −/− mice had higher EE during both the light and dark phases of the daily cycle. Respiratory quotient was lower in GHR −/− mice during the light phase, which indicated a greater utilization of lipid relative to carbohydrate in these mice. Additionally, GHR −/− mice had higher ratios of caloric intake to EE at several intervals during the dark phase, and this effect was greater and more sustained in the final three hours of the dark phase. Therefore, we conclude that GHR −/− mice are able to overcome the substantial energetic challenges of dwarfism through several mechanisms that promote stable Mb. Relative to wild type mice, the GHR −/− mice consumed more calories per unit Mb, which offset the disproportionate increase in their daily energy expenditure. While GHR −/− mice oxidized a greater proportion of lipid during the light phase in order to meet their energy requirements, they achieved greater energy efficiency and storage during the dark phase through a combination of higher energy consumption and lower LMA. PMID:19747867

  2. Anderson localization in the multi-particle tight-binding model at low energies or with weak interaction

    CERN Document Server

    Ekanga, Trésor

    2012-01-01

    We consider the multi-particle lattice Anderson model with an i.i.d. random external potential and a short-range interaction. Using the multi-particle multiscale analysis (MPMSA) developed by Chulaevsky and Suhov (2009), we prove spectral localization for such Hamiltonians at low energies under the assumption of log-H\\"{o}lder continuity of the marginal probability distribution of the random potential. Under a stronger assumption of H\\"older continuity, Anderson localization for such systems at low energies was established earlier by Aizenman and Warzel (2009) with the help of the multi-particle Fractional-Moment Method.

  3. Changes in the zero point energy of the protons as the source of the binding energy of water to A phase DNA

    CERN Document Server

    Reiter, G F; Mayers, J

    2010-01-01

    The zero point kinetic energy of protons in water is large on the scale of chemical interaction energies(29 Kj/mol in bulk room temperature water). Its value depends upon the structure of the hydrogen bond network, and can change as the network is confined or as water interacts with surfaces. These changes have been observed to be large on a chemical scale for water confined in carbon nanotubes and in the pores of xerogel, and may play a fundamental, and neglected, role in biological processes involving confined water. We measure the average momentum distribution of the protons in salmon Na-DNA using Deep Inelastic Neutron Scattering, for a weakly hydrated (6w/bp) and a dehydrated fiber sample. This permits the determination of the change in total kinetic energy of the system per water molecule removed from the DNA and placed in the bulk liquid. This energy is equal, within errors, to the measured enthalpy for the same process, demonstrating that changes in the zero point motion of the protons, arising from c...

  4. Optimizing Binding Energies of Key Intermediates for CO2 Hydrogenation to Methanol over Oxide-Supported Copper.

    Science.gov (United States)

    Kattel, Shyam; Yan, Binhang; Yang, Yixiong; Chen, Jingguang G; Liu, Ping

    2016-09-28

    Rational optimization of catalytic performance has been one of the major challenges in catalysis. Here we report a bottom-up study on the ability of TiO2 and ZrO2 to optimize the CO2 conversion to methanol on Cu, using combined density functional theory (DFT) calculations, kinetic Monte Carlo (KMC) simulations, in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) measurements, and steady-state flow reactor tests. The theoretical results from DFT and KMC agree with in situ DRIFTS measurements, showing that both TiO2 and ZrO2 help to promote methanol synthesis on Cu via carboxyl intermediates and the reverse water-gas-shift (RWGS) pathway; the formate intermediates, on the other hand, likely act as a spectator eventually. The origin of the superior promoting effect of ZrO2 is associated with the fine-tuning capability of reduced Zr(3+) at the interface, being able to bind the key reaction intermediates, e.g. *CO2, *CO, *HCO, and *H2CO, moderately to facilitate methanol formation. This study demonstrates the importance of synergy between theory and experiments to elucidate the complex reaction mechanisms of CO2 hydrogenation for the realization of a better catalyst by design.

  5. Ammonium Additives to Dissolve Lithium Sulfide through Hydrogen Binding for High-Energy Lithium–Sulfur Batteries

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Huilin; Han, Kee Sung; Vijayakumar, M.; Xiao, Jie; Cao, Ruiguo; Chen, Junzheng; Zhang, Jiguang; Mueller, Karl T.; Shao, Yuyan; Liu, Jun

    2016-07-01

    In rechargeable Li-S batteries, the uncontrollable passivation of electrodes by highly insulating Li2S limits sulfur utilization, increases polarization and decreases cycling stability. Dissolving Li2S in organic electrolyte is a facile solution to maintain the active reaction interface between electrolyte and sulfur cathode, and thus address the above issues. Herein, ammonium salts are demonstrated as effective additives to promote the dissolution of Li2S to 1.25 M in DMSO solvent at room temperature. NMR measurements show that the strong hydrogen binding effect of N-H groups plays a critical role in dissolving Li2S by forming complex ligands with S2- anions coupled with the solvent’s solvating surrounding. Ammonium additives in electrolyte can also significantly improve the oxidation kinetics of Li2S, therefore enables the direct use of Li2S as cathode material in Li-S battery system in the future. This provides a new approach to manage the solubility of lithium sulfides through cation coordination with sulfide anion.

  6. Nuclear recoil and vacuum-polarization effects on the binding energies of supercritical H-like ions

    CERN Document Server

    Aleksandrov, Ivan A; Shabaev, Vladimir M

    2015-01-01

    The Dirac Hamiltonian including nuclear recoil and vacuum-polarization operators is considered in a supercritical regime Z > 137. It is found that the nuclear recoil operator derived within the Breit approximation regularizes the Hamiltonian for the point-nucleus model and allows the ground state level to go continuously down and reach the negative energy continuum at a critical value Zcr = 145. If the Hamiltonian contains both the recoil operator and the Uehling potential, the 1s level reaches the negative energy continuum at Zcr = 144. The corresponding calculations for the excited states have been also performed. This study shows that, in contrast to previous investigations, a point-like nucleus can have effectively the charge Z > 137.

  7. Evaluation of energy spectral information in nuclear imaging and investigation of protein binding of cationic radionuclides by lactoferrin. Comprehensive progress report, October 1, 1977-September 30, 1980

    Energy Technology Data Exchange (ETDEWEB)

    Hoffer, P. B.

    1980-06-10

    Construction of an Anger camera-computer system which allows collection of both the position and energy signals from events detected by the scintillation camera has been completed. The system allows correction of energy response non-uniformity of the detector and facilitates research related to effects of energy discrimination in radionuclide scintigraphy. The system consists of electronic hardware to transmit and digitize the energy signal, software to record and process that signal in conjunction with spatial positioning signals, and additional hardware for recording the processed images so that they can be evaluated by observers. Preliminary results indicate that the system is useful in evaluating clinical images. Assymetric (eccentric) energy windows do improve image quality and are of value in improving detection of lesions on liver scintigraphs. The mechanisms by which Ga-67 is taken up in infection and tumor has been elucidated, and the uptake of radiogallium in microorganisms as a function of its interaction with siderophores was also studied. The primary function of these low molecular weight compounds is to trap ferric ion. However, gallium may be substituted for ferric ion and becomes trapped within the microorganism. The uptake of radiogallium by neutrophils and the role that lactoferrin plays in both intracellular localization of radiogallium and subsequent deposition of the radionuclide at sites of infection were also studied. Investigation of ferric ion analogs reveals definate differences in the affinity of these metals for binding molecules which helps explain their biologic activity. While ferric ion has the strongest affinity for such molecules, gallium has very high affinity for siderophores, moderate affinity for lactoferrin, and lower affinity for transferrin. The relative affinity of indium for these molecules is in approximately the reverse order.

  8. The effect of dielectric constant on binding energy and impurity self-polarization in a GaAs-Ga1- x Al x As spherical quantum dot

    Science.gov (United States)

    Mese, A. I.; Cicek, E.; Erdogan, I.; Akankan, O.; Akbas, H.

    2017-03-01

    The ground state, 1s, and the excited state, 2p, energies of a hydrogenic impurity in a GaAs-Ga1- x Al x As spherical quantum dot, are computed as a function of the donor positions. We study how the impurity self-polarization depends on the location of the impurity and the dielectric constant. The excited state anomalous impurity self-polarization in the quantum dot is found to be present in the absence of any external influence and strongly depends on the impurity position and the radius of the dot. Therefore, the excited state anomalous impurity self-polarization can give information about the impurity position in the system. Also, the variation of E_{b1s} and E_{b2p} with the dielectric constant can be utilized as a tool for finding out the correct dielectric constant of the dot material by measuring the 1s or 2p state binding energy for a fixed dot radius and a fixed impurity position.

  9. Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress

    Science.gov (United States)

    Tamarkin-Ben-Harush, Ana; Vasseur, Jean-Jacques; Debart, Françoise; Ulitsky, Igor; Dikstein, Rivka

    2017-01-01

    Transcription start-site (TSS) selection and alternative promoter (AP) usage contribute to gene expression complexity but little is known about their impact on translation. Here we performed TSS mapping of the translatome following energy stress. Assessing the contribution of cap-proximal TSS nucleotides, we found dramatic effect on translation only upon stress. As eIF4E levels were reduced, we determined its binding to capped-RNAs with different initiating nucleotides and found the lowest affinity to 5'cytidine in correlation with the translational stress-response. In addition, the number of differentially translated APs was elevated following stress. These include novel glucose starvation-induced downstream transcripts for the translation regulators eIF4A and Pabp, which are also translationally-induced despite general translational inhibition. The resultant eIF4A protein is N-terminally truncated and acts as eIF4A inhibitor. The induced Pabp isoform has shorter 5'UTR removing an auto-inhibitory element. Our findings uncovered several levels of coordination of transcription and translation responses to energy stress. DOI: http://dx.doi.org/10.7554/eLife.21907.001 PMID:28177284

  10. Excitation energy transfer and charge separation are affected in Arabidopsis thaliana mutants lacking light-harvesting chlorophyll a/b binding protein Lhcb3.

    Science.gov (United States)

    Adamiec, Małgorzata; Gibasiewicz, Krzysztof; Luciński, Robert; Giera, Wojciech; Chełminiak, Przemysław; Szewczyk, Sebastian; Sipińska, Weronika; van Grondelle, Rienk; Jackowski, Grzegorz

    2015-12-01

    The composition of LHCII trimers as well as excitation energy transfer and charge separation in grana cores of Arabidopsis thaliana mutant lacking chlorophyll a/b binding protein Lhcb3 have been investigated and compared to those in wild-type plants. In grana cores of lhcb3 plants we observed increased amounts of Lhcb1 and Lhcb2 apoproteins per PSII core. The additional copies of Lhcb1 and Lhcb2 are expected to substitute for Lhcb3 in LHCII trimers M as well as in the LHCII "extra" pool, which was found to be modestly enlarged as a result of the absence of Lhcb3. Time-resolved fluorescence measurements reveal a deceleration of the fast phase of excitation dynamics in grana cores of the mutant by ~15 ps, whereas the average fluorescence lifetime is not significantly altered. Monte Carlo modeling predicts a slowing down of the mean hopping time and an increased stabilization of the primary charge separation in the mutant. Thus our data imply that absence of apoprotein Lhcb3 results in detectable differences in excitation energy transfer and charge separation.

  11. Computation of masses and binding energies of some hadrons and bosons according to the rotating lepton model and the relativistic Newton equation

    Science.gov (United States)

    Vayenas, C. G.; Fokas, A. S.; Grigoriou, D.

    2016-08-01

    We compute analytically the masses, binding energies and hamiltonians of gravitationally bound Bohr-type states via the rotating relativistic lepton model which utilizes the de Broglie wavelength equation in conjunction with special relativity and Newton's relativistic gravitational law. The latter uses the inertial-gravitational masses, rather than the rest masses, of the rotating particles. The model also accounts for the electrostatic charge- induced dipole interactions between a central charged lepton, which is usually a positron, with the rotating relativistic lepton ring. We use three rotating relativistic neutrinos to model baryons, two rotating relativistic neutrinos to model mesons, and a rotating relativistic electron neutrino - positron (or electron) pair to model the W± bosons. It is found that gravitationally bound ground states comprising three relativistic neutrinos have masses in the baryon mass range (∼⃒ 0.9 to 1 GeV/c2), while ground states comprising two neutrinos have masses in the meson mass range (∼⃒ 0.4 to 0.8 GeV/c2). It is also found that the rest mass values of quarks are in good agreement with the heaviest neutrino mass value of 0.05 eV/c2 and that the mass of W± bosons (∼⃒ 81 GeV/c2) corresponds to the mass of a rotating gravitationally confined e± — ve pair. A generalized expression is also derived for the gravitational potential energy of such relativistic Bohr-type structures.

  12. Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase:molecular dynamics simulations and binding free energy calculations

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Acetohydroxyacid synthase(AHAS) is the target enzyme of several classes of herbicides,such as sulfonylureas and imidazolinones.Now many mutant AHASs with herbicide resistance have emerged along with extensive use of herbicides,therefore it is imperative to understand the detailed interaction mechanism and resistance mechanism so as to develop new potent inhibitors for wild-type or resistant AHAS.With the aid of available crystal structures of the Arabidopsis thaliana(At) AHAS-inhibitor complex,molecular dynamics(MD) simulations were used to investigate the interaction and resistance mechanism directly and dynamically at the atomic level.Nanosecond-level MD simulations were performed on six systems consisting of wild-type or W574L mutant AtAHAS in the complex with three sulfonylurea inhibitors,separately,and binding free energy was calculated for each system using the MM-GBSA method.Comprehensive analyses from structural and energetic aspects confirmed the importance of residue W574,and also indicated that W574L mutation might alert the structural charactersistic of the substrate access channel and decrease the binding affinity of inhibitors,which cooperatively weaken the effective channel-blocked effect and finally result in weaker inhibitory effect of inhibitor and corresponding herbicide resistance of W574L mutant.To our knowledge,it is the first report about MD simulations study on the AHAS-related system,which will pave the way to study the interactions between herbicides and wild-type or mutant AHAS dynamically,and decipher the resistance mechanism at the atomic level for better designing new potent anti-resistance herbicides.

  13. Identifying the Interaction of Vancomycin With Novel pH-Responsive Lipids as Antibacterial Biomaterials Via Accelerated Molecular Dynamics and Binding Free Energy Calculations.

    Science.gov (United States)

    Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala

    2017-03-09

    Nano-drug delivery systems have proven to be an efficient formulation tool to overcome the challenges with current antibiotics therapy and resistance. A series of pH-responsive lipid molecules were designed and synthesized for future liposomal formulation as a nano-drug delivery system for vancomycin at the infection site. The structures of these lipids differ from each other in respect of hydrocarbon tails: Lipid1, 2, 3 and 4 have stearic, oleic, linoleic, and linolenic acid hydrocarbon chains, respectively. The impact of variation in the hydrocarbon chain in the lipid structure on drug encapsulation and release profile, as well as mode of drug interaction, was investigated using molecular modeling analyses. A wide range of computational tools, including accelerated molecular dynamics, normal molecular dynamics, binding free energy calculations and principle component analysis, were applied to provide comprehensive insight into the interaction landscape between vancomycin and the designed lipid molecules. Interestingly, both MM-GBSA and MM-PBSA binding affinity calculations using normal molecular dynamics and accelerated molecular dynamics trajectories showed a very consistent trend, where the order of binding affinity towards vancomycin was lipid4 > lipid1 > lipid2 > lipid3. From both normal molecular dynamics and accelerated molecular dynamics, the interaction of lipid3 with vancomycin is demonstrated to be the weakest (∆Gbinding = -2.17 and -11.57, for normal molecular dynamics and accelerated molecular dynamics, respectively) when compared to other complexes. We believe that the degree of unsaturation of the hydrocarbon chain in the lipid molecules may impact on the overall conformational behavior, interaction mode and encapsulation (wrapping) of the lipid molecules around the vancomycin molecule. This thorough computational analysis prior to the experimental investigation is a valuable approach to guide for predicting the encapsulation

  14. Thermodynamics of fragment binding.

    Science.gov (United States)

    Ferenczy, György G; Keserű, György M

    2012-04-23

    The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.

  15. Theoretical and experimental study of the excitonic binding energy in GaAs/AlGaAs single and coupled double quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, E.M., E-mail: eldermantovani@yahoo.com.br [Departamento de Física, Química e Biologia, Universidade Estadual Paulista, C. P. 266, Presidente Prudente, São Paulo 17700-000 (Brazil); César, D.F. [Departamento de Física, Universidade Federal de São Carlos, C. P. 676, São Carlos, São Paulo (Brazil); Franchello, F.; Duarte, J.L.; Dias, I.F.L.; Laureto, E. [Departamento de Física, Universidade Estadual de Londrina, C. P. 6001, Londrina, Paraná (Brazil); Elias, D.C.; Pereira, M.V.M.; Guimarães, P.S.S. [Departamento de Física, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, C. P. 702, Belo Horizonte, Minas Gerais (Brazil); Quivy, A.A. [Laboratório de Novos Materiais Semicondutores, Instituto de Física, Universidade de São Paulo, C. P. 66318, São Paulo (Brazil)

    2013-12-15

    This paper discusses the theoretical and experimental results obtained for the excitonic binding energy (E{sub b}) in a set of single and coupled double quantum wells (SQWs and CDQWs) of GaAs/AlGaAs with different Al concentrations (Al%) and inter-well barrier thicknesses. To obtain the theoretical E{sub b} the method proposed by Mathieu, Lefebvre and Christol (MLC) was used, which is based on the idea of fractional-dimension space, together with the approach proposed by Zhao et al., which extends the MLC method for application in CDQWs. Through magnetophotoluminescence (MPL) measurements performed at 4 K with magnetic fields ranging from 0 T to 12 T, the diamagnetic shift curves were plotted and adjusted using two expressions: one appropriate to fit the curve in the range of low intensity fields and another for the range of high intensity fields, providing the experimental E{sub b} values. The effects of increasing the Al% and the inter-well barrier thickness on E{sub b} are discussed. The E{sub b} reduction when going from the SQW to the CDQW with 5 Å inter-well barrier is clearly observed experimentally for 35% Al concentration and this trend can be noticed even for concentrations as low as 25% and 15%, although the E{sub b} variations in these latter cases are within the error bars. As the Zhao's approach is unable to describe this effect, the wave functions and the probability densities for electrons and holes were calculated, allowing us to explain this effect as being due to a decrease in the spatial superposition of the wave functions caused by the thin inter-well barrier. -- Highlights: • Magnetophotoluminescence results from coupled double quantum wells are reported. • Theoretical and experimental values for excitonic binding energy (E{sub b}) are obtained. • The effects of increasing the inter-well barrier height and thickness on E{sub b} are discussed. • An E{sub b} reduction is observed when going from zero to the 5 Å inter-well barrier

  16. The hydrostatic pressure and temperature effects on hydrogenic impurity binding energies in lattice matched InP/In0.53Ga0.47As/InP square quantum well

    Science.gov (United States)

    Başer, P.; Elagoz, S.

    2017-02-01

    The on-center shallow-donor impurity binding energy in lattice matched InP/In0.53Ga0.47As square quantum well structure have been theoretically investigated using effective mass and variational techniques. The effects of hydrostatic pressure, temperature and well width has been calculated and the results are discussed.

  17. Energy

    CERN Document Server

    Foland, Andrew Dean

    2007-01-01

    Energy is the central concept of physics. Unable to be created or destroyed but transformable from one form to another, energy ultimately determines what is and isn''t possible in our universe. This book gives readers an appreciation for the limits of energy and the quantities of energy in the world around them. This fascinating book explores the major forms of energy: kinetic, potential, electrical, chemical, thermal, and nuclear.

  18. Performance of the TPSS Functional on Predicting Core Level Binding Energies of Main Group Elements Containing Molecules: A Good Choice for Molecules Adsorbed on Metal Surfaces.

    Science.gov (United States)

    Pueyo Bellafont, Noèlia; Viñes, Francesc; Illas, Francesc

    2016-01-12

    Here we explored the performance of Hartree-Fock (HF), Perdew-Burke-Ernzerhof (PBE), and Tao-Perdew-Staroverov-Scuseria (TPSS) functionals in predicting core level 1s binding energies (BEs) and BE shifts (ΔBEs) for a large set of 68 molecules containing a wide variety of functional groups for main group elements B → F and considering up to 185 core levels. A statistical analysis comparing with X-ray photoelectron spectroscopy (XPS) experiments shows that BEs estimations are very accurate, TPSS exhibiting the best performance. Considering ΔBEs, the three methods yield very similar and excellent results, with mean absolute deviations of ∼0.25 eV. When considering relativistic effects, BEs deviations drop approaching experimental values. So, the largest mean percentage deviation is of 0.25% only. Linear trends among experimental and estimated values have been found, gaining offsets with respect to ideality. By adding relativistic effects to offsets, HF and TPSS methods underestimate experimental values by solely 0.11 and 0.05 eV, respectively, well within XPS chemical precision. TPSS is posed as an excellent choice for the characterization, by XPS, of molecules on metal solid substrates, given its suitability in describing metal substrates bonds and atomic and/or molecular orbitals.

  19. Binding Procurement

    Science.gov (United States)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  20. Core-level spectra and binding energies of transition metal nitrides by non-destructive x-ray photoelectron spectroscopy through capping layers

    Science.gov (United States)

    Greczynski, G.; Primetzhofer, D.; Lu, J.; Hultman, L.

    2017-02-01

    We present the first measurements of x-ray photoelectron spectroscopy (XPS) core level binding energies (BE:s) for the widely-applicable group IVb-VIb polycrystalline transition metal nitrides (TMN's) TiN, VN, CrN, ZrN, NbN, MoN, HfN, TaN, and WN as well as AlN and SiN, which are common components in the TMN-based alloy systems. Nitride thin film samples were grown at 400 °C by reactive dc magnetron sputtering from elemental targets in Ar/N2 atmosphere. For XPS measurements, layers are either (i) Ar+ ion-etched to remove surface oxides resulting from the air exposure during sample transfer from the growth chamber into the XPS system, or (ii) in situ capped with a few nm thick Cr or W overlayers in the deposition system prior to air-exposure and loading into the XPS instrument. Film elemental composition and phase content is thoroughly characterized with time-of-flight elastic recoil detection analysis (ToF-E ERDA), Rutherford backscattering spectrometry (RBS), and x-ray diffraction. High energy resolution core level XPS spectra acquired with monochromatic Al Kα radiation on the ISO-calibrated instrument reveal that even mild etching conditions result in the formation of a nitrogen-deficient surface layer that substantially affects the extracted binding energy values. These spectra-modifying effects of Ar+ ion bombardment increase with increasing the metal atom mass due to an increasing nitrogen-to-metal sputter yield ratio. The superior quality of the XPS spectra obtained in a non-destructive way from capped TMN films is evident from that numerous metal peaks, including Ti 2p, V 2p, Zr 3d, and Hf 4f, exhibit pronounced satellite features, in agreement with previously published spectra from layers grown and analyzed in situ. In addition, the N/metal concentration ratios are found to be 25-90% higher than those obtained from the corresponding ion-etched surfaces, and in most cases agree very well with the RBS and ToF-E ERDA values. The N 1 s BE:s extracted from

  1. He-He-Ba三原子体系弱束缚态计算∗%Calculations of the binding energies of weakly b ound He-He-Ba molecules

    Institute of Scientific and Technical Information of China (English)

    勾庆东; 李勇

    2015-01-01

    The three-body Schrödinger equation is approximately solved in the hyperspherical coordinates and the binding energies of the three-body weakly bound systems are calculated with the purpose to find if He-He-Ba trimers could exist. Using the special feature of the B-spline function like the flexible and highly localized properties, hypersphercial potentials are obtained by modifying the knots distribution of the B-spline basis of different weakly bound three-atom systems. Employing the best empirical interaction potentials between each pair of particles, we obtain that in the ground state binding energies of the weakly bound typical three-atom systems, the bindings of the molecules, 4He-4He-138Ba, 4He-3He-138Ba and 3He-3He-138Ba are possible. The binding energies of these systems are shown in the order of 1 Kelvin, each system could support only one bound state. These weakly bound molecules can exist only in a very cold environment. To get insight into the geometry of the molecules, the features of the channel functions associated with the hyperspherical potential curves of each system are investigated.

  2. Energy

    CERN Document Server

    Robertson, William C

    2002-01-01

    Confounded by kinetic energy? Suspect that teaching about simple machines isn t really so simple? Exasperated by electricity? If you fear the study of energy is beyond you, this entertaining book will do more than introduce you to the topic. It will help you actually understand it. At the book s heart are easy-to-grasp explanations of energy basics work, kinetic energy, potential energy, and the transformation of energy and energy as it relates to simple machines, heat energy, temperature, and heat transfer. Irreverent author Bill Robertson suggests activities that bring the basic concepts of energy to life with common household objects. Each chapter ends with a summary and an applications section that uses practical examples such as roller coasters and home heating systems to explain energy transformations and convection cells. The final chapter brings together key concepts in an easy-to-grasp explanation of how electricity is generated. Energy is the second book in the Stop Faking It! series published by NS...

  3. Atomistic tight-binding theory of excitonic splitting energies in CdX(X = Se, S and Te)/ZnS core/shell nanocrystals

    Science.gov (United States)

    Sukkabot, Worasak; Pinsook, Udomsilp

    2017-01-01

    Using the atomistic tight-binding theory (TB) and a configuration interaction description (CI), we numerically compute the excitonic splitting of CdX(X = Se, S and Te)/ZnS core/shell nanocrystals with the objective to explain how types of the core materials and growth shell thickness can provide the detailed manipulation of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting, beneficial for the active application of quantum information. To analyze the splitting of the excitonic states, the optical band gaps, ground-state wave function overlaps and atomistic electron-hole interactions tend to be numerically demonstrated. Based on the atomistic computations, the single-particle and excitonic gaps are mainly reduced with the increasing ZnS shell thickness owing to the quantum confinement. In the range of the higher to lower energies, the order of the single-particle gaps is CdSe/ZnS, CdS/ZnS and CdTe/ZnS core/shell nanocrystals, while one of the excitonic gaps is CdS/ZnS, CdSe/ZnS and CdTe/ZnS core/shell nanocrystals because of the atomistic electron-hole interaction. The strongest electron-hole interactions are mainly observed in CdSe/ZnS core/shell nanocrystals. In addition, the computational results underline that the energies of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting are generally reduced with the increasing ZnS growth shell thickness as described by the trend of the electron-hole exchange interaction. The high-to-low splitting of the excitonic states is demonstrated in CdSe/ZnS, CdTe/ZnS and CdS/ZnS core/shell nanocrystals because of the fashion in the electron-hole exchange interaction and overlaps of the electron-hole wave functions. As the resulting calculations, it is expected that CdS/ZnS core/shell nanocrystals are the best candidates to be the source of entangled photons. Finally, the comprehensive information on the excitonic splitting can enable the use of suitable core

  4. The effects of the electric and intense laser field on the binding energies of donor impurity states (1s and 2p±) and optical absorption between the related states in an asymmetric parabolic quantum well

    Science.gov (United States)

    Kasapoglu, E.; Sakiroglu, S.; Sökmen, I.; Restrepo, R. L.; Mora-Ramos, M. E.; Duque, C. A.

    2016-10-01

    We have calculated the effects of electric and intense laser fields on the binding energies of the ground and some excited states of conduction electrons coupled to shallow donor impurities as well as the total optical absorption coefficient for transitions between 1s and 2p± electron-impurity states in a asymmetric parabolic GaAs/Ga1-x AlxAs quantum well. The binding energies were obtained using the effective-mass approximation within a variational scheme. Total absorption coefficient (linear and nonlinear absorption coefficient) for the transitions between any two impurity states were calculated from first- and third-order dielectric susceptibilities derived within a perturbation expansion for the density matrix formalism. Our results show that the effects of the electric field, intense laser field, and the impurity location on the binding energy of 1s-impurity state are more pronounced compared with other impurity states. If the well center is changed to be Lc0), the effective well width decreases (increases), and thus we can obtain the red or blue shift in the resonant peak position of the absorption coefficient by changing the intensities of the electric and non-resonant intense laser field as well as dimensions of the well and impurity positions.

  5. The effect of gap in n(k, ρ) on the single-particle properties of nucleons and the ground-state binding energy of closed-shell nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Mariji, H. [University of Coimbra, Centro de Fisica Computacional, Department of Physics, Coimbra (Portugal)

    2016-04-15

    The present work evaluates the effect of gap in the density-dependent one-body momentum distribution, n(k, ρ), at the Fermi surface on the calculation of the single-particle properties of nucleons, i.e., the momentum- and density-dependent single-particle potential and the nucleon effective mass, and also on the calculation of the ground-state binding energy of the selected closed-shell nuclei, i.e., {sup 16}O, {sup 40}Ca, and {sup 56}Ni. In order to do this, n(k, ρ) is constructed by use of the calculations of the lowest-order constrained variational method for the symmetric nuclear matter with the Av{sub 18} potential up to J{sub max} = 2 and 5. It is shown that the gap in n(k, ρ) at the Fermi surface has no significant effect on the calculation of single-particle properties in the case of J{sub max} = 5. In the relevant evaluation of the ground-state binding energy of selected nuclei, it is seen that the binding energy of {sup 16}O, improved by including n(k, ρ), is closer to the experimental data, contrary to {sup 40}Ca and {sup 56}Ni. (orig.)

  6. Localization-enhanced biexciton binding in semiconductors

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher

    1999-01-01

    The influence of excitonic localization on the binding energy of biexcitons is investigated for quasi-three-dimensional and quasi-two-dimensional AlxGa1-xAs structures. An increase of the biexciton binding energy is observed for localization energies comparable to or larger than the free biexcito...

  7. Energy

    Science.gov (United States)

    2003-01-01

    Canada, Britain, and Spain. We found that the energy industry is not in crisis ; however, U.S. government policies, laws, dollars, and even public...CEIMAT (Centro de Investagaciones Energeticas , Medioambeintales y Tecnologicas) Research and development Page 3 of 28ENERGY 8/10/04http://www.ndu.edu...meet an emerging national crisis (war), emergency (natural disaster), or major impact event (Y2K). Certain resources are generally critical to the

  8. Infinite-basis calculations of binding energies for the hydrogen bonded and stacked tetramers of formic acid and formamide and their use for validation of hybrid DFT and ab initio methods.

    Science.gov (United States)

    Zhao, Yan; Truhlar, Donald G

    2005-08-04

    Benchmark stabilization energies for planar H-bonded and stacked structures of formic acid tetramers and formamide tetramers were determined as the sum of the infinite basis set limit of MP2 energies and a CCSD(T) correction term evaluated with the 6-31G*(0.25) basis set. The infinite basis (IB) set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and separate extrapolation of the Hartree-Fock and correlation energies with new IB parameters for augmented basis sets determined here. Final stabilization energies (kcal/mol) for the tetramer studied are in the range of 4.6 to approximately 6.7 kcal/mol and they were used as reference data to test 14 density functionals. Among the tested DFT methods, PWB6K gives the best performance with an average error equal to only 30% of the average binding energy. In contrast, the popular B3LYP functional has an average error of 85%. We recommend the PWB6K method for exploring the potential energy surfaces of organic complexes and clusters and supramolecular assemblies.

  9. Diels-Alder addition of some 6-and 5-member ring aromatic compounds on the Si(001)-2×1 surface: dependence of the binding energy on the resonance energy of the aromatic compounds

    Institute of Scientific and Technical Information of China (English)

    LuXin

    2001-01-01

    [1]Onganer, Y., Saglam, M., Turut, A. et al., High barrier metallic polymer p-type silicon Schottky diodes, Solid State Electron, 1996, 39: 677.[2]Lonergan, M. C., A tunable diode based on an inorganic semiconductor vertical bar conjugated polymer interface, Science,1997, 278: 2103.[3]Wolkow, R. A., Moffatt, D. J., The frustrated motion of benzene on the surface of Si(l11), J. Chem. Phys., 1995,103: 10696.[4]MacPherson, C. D., Leung, K. T., Electron-induced chemistry of pyridine on Si(l 11)7x7 An LEED and TDS study,Surf. Sci., 1995, 324: 202.[5]MacPherson, C. D., Hu, D. Q., Leung, K. T., Room-temperature adsorption of thiophene and related 5-membered cyclicolefins on Si( 111)7x7 by thermal-desorption spectrometry, Surf. Sci., 1992, 276:156.[6]Cao, Y.. Wang, Z., Deng, J. F. et al., Evidence for dangling bond mediated dimerization of furan on the silicon (111 )-(7x7) surface, Angew Chem. Int. Ed., 2000, 39: 2740-2743.[7]Cao, Y., Yong, K. S., Wang, Z. Q. et al., Dry thienylation of the silicon (111)-(7x7) surface, J. Am. Chem. Soc., 2000, 112:1812.[8]Taguchi, Y., Fujisawa, M., Takaoka, T. et al., Adsorbed state of benzene on the Si(100) surface-thermal-desorption and electron-energy loss spectroscopy studies, J. Chem. Phys., 1991,95: 6870.[9]Lopinski, G. P., Fortier, T M., Moffatt, D. J. et al., Multiple bonding geometries and binding state conversion of benzene/Si(100), J. Vac. Sci. Technol., 1998, Al6: 1037.[10]Ellison, M. D., Hamers, R. J., Reactions of substituted aromatic hydrocarbons with the Si(001) surface, J. Vac. Sci.Technol., 2000, Al8: 1965.[11]Qiao, M. H., Cao, Y., Deng, J. F. et al, Formation of covalent Si-N linkages on pyrrole functionalized Si(100)-(2×l),Chem. Phys. Lett., 2000, 325: 508.[12]Konecny, R., Doren, D. J., Cycloaddition reactions of unsaturated hydrocarbons on the Si(100)-(2×1) surface: theoretical predictions, Surf. Sci., 1998, 417: 169.[13]Birkenheuer, U., Gutdeutsch, U., Rosch, N

  10. Threshold collision-induced dissociation of hydrated magnesium: experimental and theoretical investigation of the binding energies for Mg(2+)(H2O)x complexes (x=2-10).

    Science.gov (United States)

    Carl, Damon R; Armentrout, Peter B

    2013-03-18

    The sequential bond energies of Mg(2+)(H2O)x complexes, in which x=2-10, are measured by threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer. From an electrospray ionization source that produces an initial distribution of Mg(2+)(H2O)x complexes in which x=7-10, complexes down to x=3 are formed by using an in-source fragmentation technique. Complexes smaller than Mg(2+)(H2O)3 cannot be formed in this source because charge separation into MgOH(+)(H2O) and H3O(+) is a lower-energy pathway than simple water loss from Mg(2+)(H2O)3. The kinetic energy dependent cross sections for dissociation of Mg(2+)(H2O)x complexes, in which x=3-10, are examined over a wide energy range to monitor all dissociation products and are modeled to obtain 0 and 298 K binding energies. Analysis of both primary and secondary water molecule losses from each sized complex provides thermochemistry for the sequential hydration energies of Mg(2+) for x=2-10 and the first experimental values for x=2-4. Additionally, the thermodynamic onsets leading to the charge-separation products from Mg(2+)(H2O)3 and Mg(2+)(H2O)4 are determined for the first time. Our experimental results for x=3-7 agree well with quantum chemical calculations performed here and previously calculated binding enthalpies, as well as previous measurements for x=6. The present values for x=7-10 are slightly lower than previous experimental results and theory, but within experimental uncertainties.

  11. 铜微团簇结构及结合能的计算机模拟%Computer Simulation of the Structure and Binding Energy of Cu Micro-clusters

    Institute of Scientific and Technical Information of China (English)

    马兴科; 吕清正

    2011-01-01

    Copper cluster has many fantastic properties and is particularly interesting for their potential use in many processes like catalysis,nanotechnology and new electronic materials.Researches on the structures and binding energies of these clusters play significant roles in discussing their properties and applications.In this paper,through the study of the structures and binding energies of Cu micro-clusters(Cun(n=2,…,10)) under their stable state using the Gaussian03,based on the Density Functional Theory(DFT) and Relativistic Effective Core Potential(RECP) we find the binding energies of Cun(n=2,…,10) will increase with the increase of the value of n with rare exceptions.%铜团簇具有奇异的性质,在催化、纳米技术和大规模集成电路制造中有巨大的应用潜力.采用相对论有效原子实势模型(RECP),在密度泛函方法(DFT)下,使用Gaussian软件,研究了铜微团簇Cun(n=2,…,10)在稳态下的结构和结合能,得到了Cun(n=2,…1,0)的结合能和基态结构,发现随着n的增大,Cun(n=2,…,10)平均结合能会逐步微幅增加(极少数个体例外).

  12. Hydrostatic pressure effects on the {gamma}-X conduction band mixing and the binding energy of a donor impurity in GaAs-Ga{sub 1-x}Al{sub x}As quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Duque, C.A. [Instituto de Fisica, Universidad de Antioquia, AA 1226, Medellin (Colombia); Lopez, S.Y. [Facultad de Educacion, Universidad de Antioquia, AA 1226, Medellin (Colombia); Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001, C.P. 62210, Cuernavaca (Mexico)

    2007-06-15

    Mixing between {gamma} and X valleys of the conduction band in GaAs-Ga{sub 1-x}Al{sub x}As quantum wells is investigated taken into account the effect of applied hydrostatic pressure. This effect is introduced via the pressure-dependent values of the corresponding energy gaps and the main band parameters. The mixing is considered along the lines of a phenomenological model. Variation of the confined ground state in the well as a function of the pressure is reported. The dependencies of the variationally calculated binding energy of a donor impurity with the hydrostatic pressure and well width are also presented. It is shown that the inclusion of the {gamma}-X mixing explains the non-linear behavior in the photoluminescence peak of confined exciton states that has been observed for pressures above 20 kbar. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  13. Implications of a matter-radius measurement for the binding energy of, and existence of excited Efimov states in, Carbon-22

    CERN Document Server

    Acharya, B; Phillips, D R

    2013-01-01

    We study Borromean 2n-halo nuclei using effective field theory. We compute the universal scaling function that relates the mean-square matter radius of the 2n halo to dimensionless ratios of two- and three-body energies. We use the experimental value of the rms matter radius of 22C measured by Tanaka et al. to put constraints on its 2n separation energy and the 20C-n virtual energy. We also explore the consequences of these constraints for the existence of excited Efimov states in this nucleus. We find that, for 22C to have an rms matter radius within 1-sigma of the experimental value, the two-neutron separation energy of 22C needs to be below 100 keV. Consequently, this three-body halo system can have an excited Efimov state only if the 20C-n system has a resonance within 1 keV of the scattering threshold.

  14. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    Energy Technology Data Exchange (ETDEWEB)

    Rocklin, Gabriel J. [Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550 (United States); Mobley, David L. [Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148 (United States); Dill, Ken A. [Laufer Center for Physical and Quantitative Biology, 5252 Stony Brook University, Stony Brook, New York 11794-0001 (United States); Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich (Switzerland)

    2013-11-14

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol{sup −1}) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non

  15. Nature of the high-binding-energy dip in the low-temperature photoemission spectra of Bi sub 2 Sr sub 2 CaCu sub 2 O sub 8+. delta

    Energy Technology Data Exchange (ETDEWEB)

    Dessau, D.S.; Shen, Z.; Wells, B.O.; King, D.M.; Spicer, W.E. (Stanford Electronics Laboratory, Stanford University, Stanford, California 94305 (United States)); Arko, A.J. (Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)); Lombardo, L.W.; Mitzi, D.B.; Kapitulnik, A. (Department of Applied Physics, Stanford University, Stanford, California 94305 (United States))

    1992-03-01

    At the transition to superconductivity, an anomalous high-binding-energy ({approx}{minus}90 meV) dip appears in the low-temperature photoemission spectra taken along the {Gamma}-{ital {bar M}} high-symmetry direction of Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}}. This paper details experiments which further characterize the energy and {bold k}-space dependence of this dip structure. The dip occurs over a wide portion of the {Gamma}-{ital {bar M}} zone diagonal (110), yet shows minimal energy dispersion. In the spectra taken along the {Gamma}-{ital X} zone edge (100), the dip is very weak or not present. We show that these results imply that the dip is not an artifact dependent on the experiment or special features of the band structure and therefore is an intrinsic feature of the superconducting state of Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}}. The behavior of the normal-state bands along {Gamma}-{ital {bar M}} in relation to the local-density-approximation prediction of a Bi-O-based electron pocket'' is also discussed, with our data explained most naturally if the Bi-O band remains above the Fermi level for all {bold k}.

  16. DFT study of NH{sub 3} adsorption on the (5,0), (8,0), (5,5) and (6,6) single-walled carbon nanotubes. Calculated binding energies, NMR and NQR parameters

    Energy Technology Data Exchange (ETDEWEB)

    Shirvani, Bahram B.; Beheshtian, Javad; Esrafili, Mehdi D. [Department of Chemistry, Tarbiat Modares University, P.O. Box: 14115-175, Tehran (Iran, Islamic Republic of); Hadipour, Nasser L., E-mail: hadipour@modares.ac.i [Department of Chemistry, Tarbiat Modares University, P.O. Box: 14115-175, Tehran (Iran, Islamic Republic of)

    2010-03-15

    Behavior of a single NH{sub 3} molecule adsorbed on external surface of H-capped (5,5), (6,6), (5,0), and (8,0) single-walled carbon nanotubes (SWCNTs) is studied via DFT calculations. Binding energies clearly exhibit adsorption dependence on tube diameter. {sup 13}C, {sup 15}N and {sup 1}H chemical shielding tensors are calculated at the B3LYP level using GIAO method. NMR calculations reveal that {sup 13}C chemical shielding of (8,0) is more sensitive to NH{sub 3} adsorption compared to (5,5), (6,6) and (5,0) tubes. {sup 15}N and {sup 1}H chemical shielding correlate noticeably with diameter of the nanotubes. {sup 14}N and {sup 2}H nuclear quadrupole coupling constants, C{sub Q}, and asymmetry parameter, eta, reveal the remarkable effect of NH{sub 3} adsorption on electronic structure of the SWCNTs.

  17. Molecular evolution and binding free energy analysis on substrates of KPC carbapenemases%KPC型碳青霉烯酶分子进化及与底物结合自由能分析

    Institute of Scientific and Technical Information of China (English)

    糜祖煌; 翁幸鐾; 秦玲

    2010-01-01

    目的 分析KPC-2、KPC-5和KPC-10型碳青霉烯酶的分子进化及与10种β-内酰胺类药物的结合自由能.方法 用MEGA 4.1软件中的Minimum Evolution法分析KPC-2、KPC-5和KPC-10型碳青霉烯酶的分子进化,用ArgusLab 4.1软件中的Dock模块作这3种酶与10种β-内酰胺类药物的分子对接,并计算酶与底物的结合自由能(△G).结果 有碳青霉烯酶活性的A类β-内酰胺酶在同一簇且保守性较好,无碳青霉烯酶活性的普通A类β-内酰胺酶则在另一簇.KPC-2、KPC-5和KPC-10型碳青霉烯酶与碳青霉烯类药物结合自由能均下降,且降幅居前,它们的结合自由能比第三代头孢类抗生素更低.结合自由能较高的为氨曲南和克拉维酸.结论 KPC型碳青霉烯酶对碳青霉烯类药物的催化能力高于对第三代头孢类抗生素的催化能力,对氨曲南和克拉维酸的催化活性最低.%Objective To analyze molecular evolution and binding free energies in substrates of KPC-2,KPC-5 and KPC-10 carbapenemases.Methods Minimum Evolution method in MEGA 4.1 was used to analyze molecular evolution of KPC-2,KPC-5 and KPC-10 carbapenemases,Dock module in ArgusLab 4.1 was used to perform molecular docking of these 3 carbapenemases to 10 kinds of β-lactams substrates,and calculate binding free energies(△G).Results Ambler Class A β-lactamases with carbapenemase activities were grouped in the same cluster and had good conservation,while ordinary Ambler Class A β-lactamases without carbapenemase activities were groupod in the other cluster.Binding free energies of KPC-2,KPC-5 and KPC-10 carbapenemases were lower to carbapenem antibiotics than the thirdgeneration cephalosporins,while binding free energies to aztreonam and clavulanic acid were of comparatively higher levels.Conclusion Catalytic activities of KPC to carbapenem antibiotics are higher than those to the third-generation cephalosporins,but the activities to aztreonam and clavulanic acid are low.

  18. Positive binding energy of a biexciton confined in a localization center formed in a single InxGa1-xN/GaN quantum disk

    OpenAIRE

    Bardoux, R.; Kaneta, A.; Funato, M.; Kawakami, Y.; Kikuchi, A; Kishino, K.

    2009-01-01

    We report microphotoluminescence spectroscopy performed on individual and ensemble InGaN/GaN quantum disks (Q-disks). The typical spectrum of a single Q-disk exhibited the contribution of localization centers (LCs) formed in the InGaN active layer of the Q-disks, characterized by sharp lines appearing on the low energy side of the spectra. In addition, a broader emission peak identified as the luminescence of the quasi-two-dimensional (2D) InGaN active layer surrounding the LCs appears system...

  19. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  20. Experimental and theoretical study of the structures and binding energies of eugenol (H2O)n, n=0-2

    Science.gov (United States)

    Longarte, Asier; Unamuno, Iñigo; Fernández, José A.; Castaño, Fernando; Redondo, Carolina

    2004-07-01

    Eugenol (4-Allyl-2-methoxyphenol), a phenol-derivative with an intramolecular -OH⋯OCH3 hydrogen bond (H bond), has been studied in a supersonic expansion using a number of complementary laser spectroscopic techniques. The mass-resolved excitation spectrum of eugenol and its water complexes are reported for the first time. The most intense set of bands on the resonantly enhanced multiphoton ionization (REMPI) spectrum of eugenol originate in a conformer whose S1←S0 transition is at 35 202 cm-1 and the ionization threshold at (I0←S0) 62 544±150 cm-1 (7.755±0.019 eV). In addition, two low intensity features redshifted with respect to the 000 transition have been identified as due to a second, less stable conformer. Ab initio calculations show that the potential energy landscape depicts at least three minima associated with one folded and two extended conformers, one of which is the most stable. Clusters of eugenol/water were prepared in a supersonic expansion by seeding eugenol and water in noble gas He and examined by two-color REMPI (R2PI) and IR-UV double resonance spectroscopies. Only one single isomer was observed for both 1:1 and 1:2 complexes, in contrast with the several stable conformers provided by the computations. The dissociation energies of the 1:1 and 1:2 complexes have been determined by the fragmentation threshold method and the results compared with those from ab initio calculations conducted at the B3LYP and MP2 levels with a variety of basis sets.

  1. Energies; Energies

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

    In the framework of the National Debate on the energies in a context of a sustainable development some associations for the environment organized a debate on the nuclear interest facing the renewable energies. The first part presents the nuclear energy as a possible solution to fight against the greenhouse effect and the associated problem of the wastes management. The second part gives information on the solar energy and the possibilities of heat and electric power production. A presentation of the FEE (French wind power association) on the situation and the development of the wind power in France, is also provided. (A.L.B.)

  2. ADC-57型头孢菌素酶分子进化及与底物结合自由能分析%Molecular evolution and binding free energy analysis of substrates of cephalosporinase ADC-57

    Institute of Scientific and Technical Information of China (English)

    周军; 王玉月; 张秋娣

    2012-01-01

    Objective To analyze molecular evolution and binding free energies of cephalosporinase ADC-57.Methods Minimum Evolution method in MEGA 5.0 was used to analyze molecular evolution of cephalosporinase ADC-57 and other 19 kinds of beta-lactamases.Tertiary structure of ADC-57 was predicted by homology modeling referring to tertiary structure of CMY-2.The molecular docking of ADC-57 to 11kinds of beta-lactams substrates was performed using DOCK module in ArgusLab 4.1and the binding free energies (△G) was calculated.Results ADC-57,CMY-2,DHA-1,ADC-7,ADC-56 were all belong to class C beta-lactamase,and molecular evolution between ADC-57 and ADC-56 was closest.The top three antibiotics with declining binding free energy of beta-lactams were ertapenem,cefoxitin and ceftazidine,while the last two were clavulanic acid and aztreonam.Conclusions Catalytic activities of cephalosporinase ADC-57 to ertapenem,cefoxitin and ceftazidine are high,while to clavulanic acid and aztreonam are low. Hydrolytic activities of enzyme to beta-lactams (substrates) can be analyzed by molecular docking.%目的 分析ADC-57型头孢菌素酶分子进化及其对各种底物的结合自由能.方法 用MEGA 5.0软件中的最小进化法分析ADC-57和其他19种β-内酰胺酶的分子进化,参照同类酶CMY-2型酶作同源建模获得ADC67型头孢菌素酶分子的3D结构,并用ArgusLab 4.1软件中的DOCK模块作ADC-57型头孢菌素酶与11种β-内酰胺类药物底物的分子对接,最后计算酶与底物的结合自由能值(△G).结果 ADC-57与CMY-2、DHA-1、ADC-7、ADC-56归属为C类β-内酰胺酶,均为头孢菌素酶,且与ADC-56关系最为密切.ADC-57与β-内酰胺类药物结合自由能下降居前3位的为厄他培南、头孢西丁和头孢他啶,结合自由能下降排在后2位的为克拉维酸和氨曲南.结论 ADC-57型头孢菌素酶对厄他培南、头孢西丁和头孢他啶的催化能力高,而对克拉维酸和氨曲南的催化能力低.分子对接

  3. Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

    DEFF Research Database (Denmark)

    Færgeman, Nils J.; Sigurskjold, B W; Kragelund, B B

    1996-01-01

    Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl......-CoA esters containing more than eight carbon atoms and that the 3'-phosphate of the ribose accounts for almost half of the binding energy. Binding of acyl-CoA esters, with increasing chain length, to ACBP was clearly enthalpically driven with a slightly unfavorable entropic contribution. Accessible surface...... areas derived from the measured enthalpies were compared to those calculated from sets of three-dimensional solution structures and showed reasonable correlation, confirming the enthalphically driven binding. Binding of dodecanoyl-CoA to ACBP was studied at various temperatures and was characterized...

  4. Membrane binding domains

    OpenAIRE

    Hurley, James H.

    2006-01-01

    Eukaryotic signaling and trafficking proteins are rich in modular domains that bind cell membranes. These binding events are tightly regulated in space and time. The structural, biochemical, and biophysical mechanisms for targeting have been worked out for many families of membrane binding domains. This review takes a comparative view of seven major classes of membrane binding domains, the C1, C2, PH, FYVE, PX, ENTH, and BAR domains. These domains use a combination of specific headgroup inter...

  5. Is there a link between selectivity and binding thermodynamics profiles?

    Science.gov (United States)

    Tarcsay, Ákos; Keserű, György M

    2015-01-01

    Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding.

  6. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  7. Binding capacity: cooperativity and buffering in biopolymers.

    Science.gov (United States)

    Di Cera, E; Gill, S J; Wyman, J

    1988-01-01

    The group of linkage potentials resulting from the energy of a physicochemical system expressed per mol of a reference component, say a polyfunctional macromolecule, leads to the concept of binding capacity. This concept applies equally to both chemical and physical ligands and opens the way to consideration of higher-order linkage relationships. It provides a means of exploring the consequences of thermodynamic stability on generalized binding phenomena in biopolymers. PMID:3422436

  8. Ureaplasma urealyticum binds mannose-binding lectin.

    Science.gov (United States)

    Benstein, Barbara D; Ourth, Donald D; Crouse, Dennis T; Shanklin, D Radford

    2004-10-01

    Mannose-binding C-type lectin (MBL) is an important component of innate immunity in mammals. Mannose-binding lectin (MBL), an acute phase protein, acts as an opsonin for phagocytosis and also activates the mannan-binding lectin complement pathway. It may play a particularly significant role during infancy before adequate specific protection can be provided by the adaptive immune system. Ureaplasma urealyticum has been linked to several diseases including pneumonia and chronic lung disease (CLD) in premature infants. We therefore investigated the ability of U. urealyticum to bind MBL. A guinea pig IgG anti-rabbit-MBL antiserum was produced. An immunoblot (dot-blot) assay done on nitrocellulose membrane determined that the anti-MBL antibody had specificity against both rabbit and human MBL. Pure cultures of U. urealyticum, serotype 3, were used to make slide preparations. The slides containing the organisms were then incubated with nonimmune rabbit serum containing MBL. Ureaplasma was shown to bind rabbit MBL with an immunocytochemical assay using the guinea pig IgG anti-rabbit MBL antiserum. Horseradish peroxidase (HRP)-labeled anti-guinea pig IgG was used to localize the reaction. The anti-MBL antiserum was also used in an immunocytochemical assay to localize U. urealyticum in histological sections of lungs from mice specifically infected with this organism. The same method also indicated binding of MBL by ureaplasma in human lung tissue obtained at autopsy from culture positive infants. Our results demonstrate that ureaplasma has the capacity to bind MBL. The absence of MBL may play a role in the predisposition of diseases related to this organism.

  9. Ligand binding mechanics of maltose binding protein.

    Science.gov (United States)

    Bertz, Morten; Rief, Matthias

    2009-11-13

    In the past decade, single-molecule force spectroscopy has provided new insights into the key interactions stabilizing folded proteins. A few recent studies probing the effects of ligand binding on mechanical protein stability have come to quite different conclusions. While some proteins seem to be stabilized considerably by a bound ligand, others appear to be unaffected. Since force acts as a vector in space, it is conceivable that mechanical stabilization by ligand binding is dependent on the direction of force application. In this study, we vary the direction of the force to investigate the effect of ligand binding on the stability of maltose binding protein (MBP). MBP consists of two lobes connected by a hinge region that move from an open to a closed conformation when the ligand maltose binds. Previous mechanical experiments, where load was applied to the N and C termini, have demonstrated that MBP is built up of four building blocks (unfoldons) that sequentially detach from the folded structure. In this study, we design the pulling direction so that force application moves the two MBP lobes apart along the hinge axis. Mechanical unfolding in this geometry proceeds via an intermediate state whose boundaries coincide with previously reported MBP unfoldons. We find that in contrast to N-C-terminal pulling experiments, the mechanical stability of MBP is increased by ligand binding when load is applied to the two lobes and force breaks the protein-ligand interactions directly. Contour length measurements indicate that MBP is forced into an open conformation before unfolding even if ligand is bound. Using mutagenesis experiments, we demonstrate that the mechanical stabilization effect is due to only a few key interactions of the protein with its ligand. This work illustrates how varying the direction of the applied force allows revealing important details about the ligand binding mechanics of a large protein.

  10. Theoretical studies of binding of mannose-binding protein to monosaccharides

    Science.gov (United States)

    Aida-Hyugaji, Sachiko; Takano, Keiko; Takada, Toshikazu; Hosoya, Haruo; Kojima, Naoya; Mizuochi, Tsuguo; Inoue, Yasushi

    2004-11-01

    Binding properties of mannose-binding protein (MBP) to monosaccharides are discussed based on ab initio molecular orbital calculations for cluster models constructed. The calculated binding energies indicate that MBP has an affinity for N-acetyl- D-glucosamine, D-mannose, L-fucose, and D-glucose rather than D-galactose and N-acetyl- D-galactosamine, which is consistent with the biochemical experimental results. Electrostatic potential surfaces at the binding site of four monosaccharides having binding properties matched well with that of MBP. A vacant frontier orbital was found to be localized around the binding site of MBP, suggesting that MBP-monosaccharide interaction may occur through electrostatic and orbital interactions.

  11. Protein Binding Pocket Dynamics.

    Science.gov (United States)

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  12. Isothermal titration calorimetry: general formalism using binding polynomials.

    Science.gov (United States)

    Freire, Ernesto; Schön, Arne; Velazquez-Campoy, Adrian

    2009-01-01

    The theory of the binding polynomial constitutes a very powerful formalism by which many experimental biological systems involving ligand binding can be analyzed under a unified framework. The analysis of isothermal titration calorimetry (ITC) data for systems possessing more than one binding site has been cumbersome because it required the user to develop a binding model to fit the data. Furthermore, in many instances, different binding models give rise to identical binding isotherms, making it impossible to discriminate binding mechanisms using binding data alone. One of the main advantages of the binding polynomials is that experimental data can be analyzed by employing a general model-free methodology that provides essential information about the system behavior (e.g., whether there exists binding cooperativity, whether the cooperativity is positive or negative, and the magnitude of the cooperative energy). Data analysis utilizing binding polynomials yields a set of binding association constants and enthalpy values that conserve their validity after the correct model has been determined. In fact, once the correct model is validated, the binding polynomial parameters can be immediately translated into the model specific constants. In this chapter, we describe the general binding polynomial formalism and provide specific theoretical and experimental examples of its application to isothermal titration calorimetry.

  13. Python bindings for libcloudph++

    OpenAIRE

    Jarecka, Dorota; Arabas, Sylwester; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python ...

  14. Python bindings for libcloudph++

    CERN Document Server

    Jarecka, Dorota; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python bindings to access libcloudph++ from Fortran is presented.

  15. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

    The DNS & BIND Cookbook presents solutions to the many problems faced by network administrators responsible for a name server. Following O'Reilly's popular problem-and-solution cookbook format, this title is an indispensable companion to DNS & BIND, 4th Edition, the definitive guide to the critical task of name server administration. The cookbook contains dozens of code recipes showing solutions to everyday problems, ranging from simple questions, like, "How do I get BIND?" to more advanced topics like providing name service for IPv6 addresses. It's full of BIND configuration files that yo

  16. On Binding Domains

    NARCIS (Netherlands)

    Everaert, M.B.H.

    2005-01-01

    In this paper I want to explore reasons for replacing Binding Theory based on the anaphor-pronoun dichotomy by a Binding Theory allowing more domains restricting/defining anaphoric dependencies. This will, thus, have consequences for the partitioning of anaphoric elements, presupposing more types of

  17. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  18. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  19. SHBG (Sex Hormone Binding Globulin)

    Science.gov (United States)

    ... as: Testosterone-estrogen Binding Globulin; TeBG Formal name: Sex Hormone Binding Globulin Related tests: Testosterone , Free Testosterone, ... I should know? How is it used? The sex hormone binding globulin (SHBG) test may be used ...

  20. The Elastic Continuum Limit of the Tight Binding Model

    Institute of Scientific and Technical Information of China (English)

    Weinan E; Jianfeng LU

    2007-01-01

    The authors consider the simplest quantum mechanics model of solids, the tight binding model, and prove that in the continuum limit, the energy of tight binding model converges to that of the continuum elasticity model obtained using Cauchy-Born rule. Thet echnique in this paper is based mainly on spectral perturbation theory for large matrices.

  1. CARBOHYDRATE-CONTAINING COMPOUNDS WHICH BIND TO CARBOHYDRATE BINDING RECEPTORS

    DEFF Research Database (Denmark)

    1995-01-01

    Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases.......Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases....

  2. Tension-induced binding of semiflexible biopolymers

    CERN Document Server

    Benetatos, Panayotis; Zippelius, Annette

    2014-01-01

    We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with a sequence of inter-chain binding sites regularly spaced along the contours. Reversible cross-links attach and detach at the sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and find the emergence of a free-energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the tension increases. We show that this transition is related to the cross-over between weak and strong localization of a directed polymer in a pinning potential. The cross-over to the strongly bound state can be interpreted as a mechan...

  3. Study of the influence of chemical binding on resonant absorption and scattering of neutrons; Etude de l'influence des liaisons chimiques sur l'absorption et la diffusion des neutrons aux energies de resonance

    Energy Technology Data Exchange (ETDEWEB)

    Naberejnev, D.G. [Aix-Marseille-1 Univ., 13 - Marseille (France)

    1999-02-01

    At present time the problem of taking into account of the crystalline binding in the heavy nuclei resonance range is not correctly treated in nuclear data processing codes. The present work deals separately with resonant absorption and scattering of neutrons. The influence of crystalline binding is considered for both types of reactions in the harmonic crystal frame work. The harmonic crystal model is applied to the study of resonant absorption cross sections to show the inconsistency of the free gas model widely in use in reactor neutronics. The errors due to the use of the latter were found to be non negligible. These errors should be corrected by introducing a more elaborated harmonic crystal model in codes for resonances analysis and on the nuclear data processing stage. Currently the influence of crystalline binding on transfer cross section in the resonance domain is taken into account in a naive manner using the model of the free nucleus at rest in the laboratory system. In this work I present a formalism (Uncoupled Phonon Approximation) which permits to consider in more detail the crystalline structure of the nuclear fuel. This formalism shows new features in comparison with the static model. (author)

  4. A statistical mechanics handbook for protein-ligand binding simulation.

    Science.gov (United States)

    Rocchia, Walter; Bonella, Sara

    2013-01-01

    In this work, the fundamental elements of statistical mechanics underlying the simulation of the protein-ligand binding process, such as statistical ensembles and the concept of microscopic estimators of macroscopic observables and free energy, are summarized in a self consistent fashion. Particular attention is then devoted to the introduction of some mathematical tools that are used in atomistic simulations aimed at estimating binding affinities and free energy profiles, and to the illustration of the origins of the difficulties encountered in this endeavor.

  5. An accurate and efficient computational protocol for obtaining the complete basis set limits of the binding energies of water clusters at the MP2 and CCSD(T) levels of theory: Application to (H2O)m, m = 2-6, 8, 11, 16, and 17.

    Science.gov (United States)

    Miliordos, Evangelos; Xantheas, Sotiris S

    2015-06-21

    We report MP2 and Coupled Cluster Singles, Doubles, and perturbative Triples [CCSD(T)] binding energies with basis sets up to pentuple zeta quality for the (H2O)m=2-6,8 water clusters. Our best CCSD(T)/Complete Basis Set (CBS) estimates are -4.99 ± 0.04 kcal/mol (dimer), -15.8 ± 0.1 kcal/mol (trimer), -27.4 ± 0.1 kcal/mol (tetramer), -35.9 ± 0.3 kcal/mol (pentamer), -46.2 ± 0.3 kcal/mol (prism hexamer), -45.9 ± 0.3 kcal/mol (cage hexamer), -45.4 ± 0.3 kcal/mol (book hexamer), -44.3 ± 0.3 kcal/mol (ring hexamer), -73.0 ± 0.5 kcal/mol (D2d octamer), and -72.9 ± 0.5 kcal/mol (S4 octamer). We have found that the percentage of both the uncorrected (De) and basis set superposition error-corrected (De (CP)) binding energies recovered with respect to the CBS limit falls into a narrow range on either sides of the CBS limit for each basis set for all clusters. In addition, this range decreases upon increasing the basis set. Relatively accurate estimates (within set) or the "12, 12" (for the AVTZ, AVQZ, and AV5Z sets) mixing ratio between De and De (CP). These mixing rations are determined via a least-mean-squares approach from a dataset that encompasses clusters of various sizes. Based on those findings, we propose an accurate and efficient computational protocol that can be presently used to estimate accurate binding energies of water clusters containing up to 30 molecules (for CCSD(T)) and up to 100 molecules (for MP2).

  6. Relating the shape of protein binding sites to binding affinity profiles: is there an association?

    Directory of Open Access Journals (Sweden)

    Bitter István

    2010-10-01

    Full Text Available Abstract Background Various pattern-based methods exist that use in vitro or in silico affinity profiles for classification and functional examination of proteins. Nevertheless, the connection between the protein affinity profiles and the structural characteristics of the binding sites is still unclear. Our aim was to investigate the association between virtual drug screening results (calculated binding free energy values and the geometry of protein binding sites. Molecular Affinity Fingerprints (MAFs were determined for 154 proteins based on their molecular docking energy results for 1,255 FDA-approved drugs. Protein binding site geometries were characterized by 420 PocketPicker descriptors. The basic underlying component structure of MAFs and binding site geometries, respectively, were examined by principal component analysis; association between principal components extracted from these two sets of variables was then investigated by canonical correlation and redundancy analyses. Results PCA analysis of the MAF variables provided 30 factors which explained 71.4% of the total variance of the energy values while 13 factors were obtained from the PocketPicker descriptors which cumulatively explained 94.1% of the total variance. Canonical correlation analysis resulted in 3 statistically significant canonical factor pairs with correlation values of 0.87, 0.84 and 0.77, respectively. Redundancy analysis indicated that PocketPicker descriptor factors explain 6.9% of the variance of the MAF factor set while MAF factors explain 15.9% of the total variance of PocketPicker descriptor factors. Based on the salient structures of the factor pairs, we identified a clear-cut association between the shape and bulkiness of the drug molecules and the protein binding site descriptors. Conclusions This is the first study to investigate complex multivariate associations between affinity profiles and the geometric properties of protein binding sites. We found that

  7. Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin.

    Science.gov (United States)

    Zhang, Zhisen; Santos, Andrew P; Zhou, Qing; Liang, Lijun; Wang, Qi; Wu, Tao; Franzen, Stefan

    2016-04-01

    The binding free energy of 4-bromophenol (4-BP), an inhibitor that binds in the internal binding site in dehaloperoxidase-hemoglobin (DHP) was calculated using Molecular Dynamics (MD) methods combined with pulling or umbrella sampling. The effects of systematic changes in the pulling speed, pulling force constant and restraint force constant on the calculated potential of mean force (PMF) are presented in this study. The PMFs calculated using steered molecular dynamics (SMD) were validated by umbrella sampling (US) in the strongly restrained regime. A series of restraint force constants ranging from 1000 down to 5 kJ/(mol nm(2)) were used in SMD simulations. This range was validated using US, however noting that weaker restraints give rise to a broader sampling of configurations. This comparison was further tested by a pulling simulation conducted without any restraints, which was observed to have a value closest to the experimentally measured free energy for binding of 4-BP to DHP based on ultraviolet-visible (UV-vis) and resonance Raman spectroscopies. The protein-inhibitor system is well suited for fundamental study of free energy calculations because the DHP protein is relatively small and the inhibitor is quite rigid. Simulation configuration structures are compared to the X-ray crystallography structures of the binding site of 4-BP in the distal pocket above the heme.

  8. Defining Starch Binding by Glucan Phosphatases

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper;

    2015-01-01

    Starch is a vital energy molecule in plants that has a wide variety of uses in industry, such as feedstock for biomaterial processing and biofuel production. Plants employ a three enzyme cyclic process utilizing kinases, amylases, and phosphatases to degrade starch in a diurnal manner. Starch...... is comprised of the branched glucan amylopectin and the more linear glucan amylose. Our lab has determined the first structures of these glucan phosphatases and we have defined their enzymatic action. Despite this progress, we lacked a means to quickly and efficiently quantify starch binding to glucan...... phosphatases. The main objective of this study was to quantify the binding affinity of different enzymes that are involved in this cyclic process. We established a protocol to quickly, reproducibly, and quantitatively measure the binding of the enzymes to glucans utilizing Affinity Gel Electrophoresis (AGE...

  9. Terms of Binding

    NARCIS (Netherlands)

    Sevcenco, A.

    2006-01-01

    The present dissertation aimed at achieving two goals. First, it constitutes an attempt to widen the search for phenomena that bear relevance to the idea that binding has a syntactic residue and is not, therefore, an exclusively semantic matter. Second, it tried to provide the technical means to acc

  10. Binding and Bulgarian

    NARCIS (Netherlands)

    Schürcks-Grozeva, Lilia Lubomirova

    2003-01-01

    In haar proefschrift analyseert Lilia Schürcks de anaforische verschijnselen in de Bulgaarse taal. Het gaat dan om wederkerende aspecten, uitgedrukt bij woorden als ‘zich’ en ‘elkaar’. De situatie in het Bulgaars blijkt moeilijk in te passen in de klassieke Binding Theory van Noam Chomsky. Bron: RUG

  11. MD-2 binds cholesterol.

    Science.gov (United States)

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I

    2016-02-19

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis.

  12. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  13. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  14. Megalin binds and mediates cellular internalization of folate binding protein

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan;

    2005-01-01

    Folate is an essential vitamin involved in a number of biological processes. High affinity folate binding proteins (FBPs) exist both as glycosylphosphatidylinositol-linked, membrane associated folate binding proteins and as soluble FBPs in plasma and some secretory fluids such as milk, saliva...... to bind and mediate cellular uptake of FBP. Surface plasmon resonance analysis shows binding of bovine and human milk FBP to immobilized megalin, but not to low density lipoprotein receptor related protein. Binding of (125)I-labeled folate binding protein (FBP) to sections of kidney proximal tubule, known...

  15. Chiral morphology of calcite through selective binding of amino acids

    Science.gov (United States)

    Orme, Christine

    2002-03-01

    Many living organisms contain biominerals and composites with finely tuned properties, reflecting a remarkable level of control over the nucleation, growth and shape of the constituent crystals. Peptides and proteins play an important role in achieving this control. Using in situ AFM we find that site-specific binding of amino acid residues to surface steps changes the step-edge free energies, giving rise to direction-specific binding energies unique to individual amino acid enantiomers and leading to chiral modifications that propagate from atomic length scales to macroscopic length scales. Molecular modeling studies support an energetic basis for the differences in binding. Our results emphasize that the mechanism under-lying crystal modification through organic molecules is best understood by considering both stereochemical recognition as well as the effects of binding on the interfacial energies of the growing crystal.

  16. Different thermodynamic signatures for DNA minor groove binding with changes in salt concentration and temperature.

    Science.gov (United States)

    Wang, Shuo; Kumar, Arvind; Aston, Karl; Nguyen, Binh; Bashkin, James K; Boykin, David W; Wilson, W David

    2013-10-04

    The effects of salt concentration and temperature on the thermodynamics of DNA minor groove binding have quite different signatures: binding enthalpy is salt concentration independent but temperature dependent. Conversely, binding free energy is salt dependent but essentially temperature independent through enthalpy-entropy compensation.

  17. Different Thermodynamic Signatures for DNA Minor Groove Binding with Changes in Salt Concentration and Temperature

    OpenAIRE

    2013-01-01

    The effects of salt concentration and temperature on the thermodynamics of DNA minor groove binding have quite different signatures: binding enthalpy is salt concentration independent but temperature dependent. Conversely, binding free energy is salt dependent but essentially temperature independent through enthalpy-entropy compensation.

  18. Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

    Science.gov (United States)

    Tran, Diem-Trang T.; Le, Ly T.; Truong, Thanh N.

    2013-08-01

    Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.

  19. Binding Principles A and B

    Institute of Scientific and Technical Information of China (English)

    陈源

    2014-01-01

    This paper focuses on the discussion of how Binding Principle A and Binding Principe B help with the interpretation of reference in English and Chinese. They are supposedly universal across languages.

  20. Ethylene binding to Au/Cu alloy nanoparticles

    Science.gov (United States)

    Gammage, Michael D.; Stauffer, Shannon; Henkelman, Graeme; Becker, Michael F.; Keto, John W.; Kovar, Desiderio

    2016-11-01

    Weak chemisorption of ethylene has been shown to be an important characteristic in the use of metals for the separation of ethylene from ethane. Previously, density functional theory (DFT) has been used to predict the binding energies of various metals and alloys, with Ag having the lowest chemisorption energy amongst the metals and alloys studied. Here Au/Cu alloys are investigated by a combination of DFT calculations and experimental measurements. It is inferred from experiments that the binding energy between a Au/Cu alloy and ethylene is lower than to either of the pure metals, and DFT calculations confirm that this is the case when Au segregates to the particle surface. Implications of this work suggest that it may be possible to further tune the binding energy with ethylene by compositional and morphological control of films produced from Au-surface segregated alloys.

  1. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

    Tanley, Simon W. M. [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom); Diederichs, Kay [University of Konstanz, D-78457 Konstanz (Germany); Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Levy, Colin [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Helliwell, John R., E-mail: john.helliwell@manchester.ac.uk [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom)

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  2. Correlation between catalytic activity of supported gold catalysts for carbon monoxide oxidation and metal-oxygen binding energy of the support metal oxides%负载金催化剂上CO氧化反应活性与金属氧化物载体中金属-氧结合能之间的关系

    Institute of Scientific and Technical Information of China (English)

    Takashi Fujita; Masanori Horikawa; Takashi Takei; Toru Murayama; Masatake Haruta

    2016-01-01

    The effect of a wide variety of metal oxide (MOx) supports has been discussed for CO oxidation on nanoparticulate gold catalysts. By using typical co‐precipitation and deposition–precipitation methods and under identical calcination conditions, supported gold catalysts were prepared on a wide variety of MOx supports, and the temperature for 50%conversion was measured to qualita‐tively evaluate the catalytic activities of these simple MOx and supported Au catalysts. Furthermore, the difference in these temperatures for the simple MOx compared to the supported Au catalysts is plotted against the metal–oxygen binding energies of the support MOx. A clear volcano‐like correla‐tion between the temperature difference and the metal–oxygen binding energies is observed. This correlation suggests that the use of MOx with appropriate metal–oxygen binding energies (300–500 kJ/atom O) greatly improves the catalytic activity of MOx by the deposition of Au NPs.%讨论了金属氧化物载体(MOx)对其负载纳米金催化剂(Au/MOx)上CO氧化反应的影响。采用典型的共沉淀法和沉积-沉淀法在完全相同的焙烧条件下制备了一系列MOx负载金催化剂,以CO氧化转化50%时的反应温度(T1/2)定量评价了MOx载体和Au/MOx催化剂的催化活性。进一步将MOx载体与相应Au/MOx催化剂的T1/2值之差对MOx载体的金属-氧结合能做曲线进行关联,发现二者呈明显的火山型关系。这一结果表明,采用具有适当金属-氧结合能(300–500 atom O)的MOx可大大提高沉积于其上的Au纳米颗粒的催化活性。

  3. Highly selective ligand binding by Methylophilus methylotrophus cytochrome c''.

    Science.gov (United States)

    Quintas, Pedro O; Catarino, Teresa; Todorovic, Smilja; Turner, David L

    2011-06-28

    Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. Despite cyt c'' having an axial site available for binding small ligands, we show here that only NO binds readily to the ferrous cyt c''. Binding of CO, as well as CN(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. Standard free energies for the binding of NO and CO reveal high selectivity of the ferrous cyt c'' for NO, indicating its putative physiological role. In this work, we characterize in detail the kinetics of NO binding and the structural features of the Fe(2+)-NO adduct by stopped-flow and resonance Raman spectroscopy, respectively.

  4. Roles of multiple surface sites, long substrate binding clefts, and carbohydrate binding modules in the action of amylolytic enzymes on polysaccharide substrates

    DEFF Research Database (Denmark)

    Nielsen, Morten Munch; Seo, E.S.; Dilokpimol, Adiphol

    2008-01-01

    with a characteristic subsite binding energy profile around the catalytic site. Furthermore, several amylolytic enzymes that facilitate attack on the natural substrate, i.e. the endosperm starch granules, have secondary sugar binding sites either situated on the surface of the protein domain or structural unit...... that contains the catalytic site or belonging to a separate starch binding domain. The role of surface sites in the function of barley alpha-amylase 1 has been investigated by using mutational analysis in conjunction with carbohydrate binding analyses and crystallography. The ability to bind starch depends...

  5. Development of a glucose binding protein biosensor

    Science.gov (United States)

    Dweik, M.; Milanick, M.; Grant, S.

    2007-09-01

    Glucose binding protein (GBP) is a monomeric periplasmic protein. It is synthesized in the cytoplasm of Escherichia coli which functions as a receptor for transport D-glucose. GBP binds glucose with high affinity. The binding mechanism is based on a hinge motion due to the protein conformational change. This change was utilized as an optical sensing mechanism by applying Fluorescence Resonance Energy Transfer (FRET). The wild-type GBP lacks cysteine in its structure, but by introducing a single cysteine at a specific site by site-directed mutagenesis, this ensured single-label attachment at specific sites with a fluorescent probe. The other sites were amino sites, which were labeled with second fluorophore. The near IR FRET pair, Alexa Fluor 680 (AF680) and Alexa Fluor 750(AF750), was utilized. The AF680 targeted the amine sites, which was the donor fluorophore, while the AF750 labeled the single cysteine site, which was the acceptor fluorophore. The sensing system strategy was based on the fluorescence changes of the probe as the protein undergoes a structural change upon binding. This biosensor had the ability to detect down to 10 uM concentrations of glucose. Next the probes were uploaded into red blood cells via hypo osmotic dialysis. The sensor responded to glucose while encapsulated with the red cells. These results showed the feasibility of an intracellular glucose biosensor.

  6. Configuration Interaction calculations of positron binding to Be(3Po)

    CERN Document Server

    Bromley, M W J

    2006-01-01

    The Configuration Interaction method is applied to investigate the possibility of positron binding to the metastable beryllium (1s^22s2p 3Po) state. The largest calculation obtained an estimated energy that was unstable by 0.00014 Hartree with respect to the Ps + Be^+(2s) lowest dissociation channel. It is likely that positron binding to parent states with non-zero angular momentum is inhibited by centrifugal barriers.

  7. Binding of several benzodiazepines to bovine serum albumin: Fluorescence study

    Science.gov (United States)

    Machicote, Roberta G.; Pacheco, María E.; Bruzzone, Liliana

    2010-10-01

    The interactions of lorazepam, oxazepam and bromazepam with bovine serum albumin (BSA) were studied by fluorescence spectrometry. The Stern-Volmer quenching constants and corresponding thermodynamic parameters Δ H, Δ G and Δ S were calculated. The binding constants and the number of binding sites were also investigated. The distances between the donor (BSA) and the acceptors (benzodiazepines) were obtained according to fluorescence resonance energy transfer and conformational changes of BSA were observed from synchronous fluorescence spectra.

  8. Effects of water models on binding affinity: evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase.

    Science.gov (United States)

    Nguyen, Trang Truc; Viet, Man Hoang; Li, Mai Suan

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔG(bind) of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔG(bind) is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔG(bind) decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM.

  9. Analytic QCD Binding Potentials

    CERN Document Server

    Fried, H M; Grandou, T; Sheu, Y -M

    2011-01-01

    This paper applies the analytic forms of a recent non-perturbative, manifestly gauge- and Lorentz-invariant description (of the exchange of all possible virtual gluons between quarks ($Q$) and/or anti-quarks ($\\bar{Q}$) in a quenched, eikonal approximation) to extract analytic forms for the binding potentials generating a model $Q$-$\\bar{Q}$ "pion", and a model $QQQ$ "nucleon". Other, more complicated $Q$, $\\bar{Q}$ contributions to such color-singlet states may also be identified analytically. An elementary minimization technique, relevant to the ground states of such bound systems, is adopted to approximate the solutions to a more proper, but far more complicated Schroedinger/Dirac equation; the existence of possible contributions to the pion and nucleon masses due to spin, angular momentum, and "deformation" degrees of freedom is noted but not pursued. Neglecting electromagnetic and weak interactions, this analysis illustrates how the one new parameter making its appearance in this exact, realistic formali...

  10. Binding characteristics of salbutamol with DNA by spectral methods

    Science.gov (United States)

    Bi, Shuyun; Pang, Bo; Zhao, Tingting; Wang, Tianjiao; Wang, Yu; Yan, Lili

    2013-07-01

    Salbutamol interacting with deoxyribonucleic acid (DNA) was examined by fluorescence, UV absorption, viscosity measurements, and DNA melting techniques. The binding constants and binding sites were obtained at different temperatures by fluorescence quenching. The Stern-Volmer plots showed that the quenching of fluorescence of salbutamol by DNA was a static quenching. To probe the binding mode, various analytical methods were performed and the results were as follows: hyperchromic effect was shown in the absorption spectra of salbutamol upon addition of DNA; there was no appreciable increase in melting temperature of DNA when salbutamol was presented in DNA solution; the fluorescence intensity of salbutamol-DNA decrease with the increasing ionic strength; the relative viscosity of DNA did not change in the presence of salbutamol; the binding constant of salbutamol with double strand DNA (dsDNA) was much higher than that of it with single strand DNA (ssDNA). All these results indicated that the binding mode of salbutamol to DNA should be groove binding. The thermodynamic parameters suggested that hydrogen bond or van der Waals force might play an important role in salbutamol binding to DNA. According to the Förster energy transference theory, the binding distance between the acceptor and donor was 3.70 nm.

  11. Entropic and enthalpic contributions to annexin V-membrane binding: a comprehensive quantitative model.

    Science.gov (United States)

    Jeppesen, Brian; Smith, Christina; Gibson, Donald F; Tait, Jonathan F

    2008-03-07

    Annexin V binds to membranes with very high affinity, but the factors responsible remain to be quantitatively elucidated. Analysis by isothermal microcalorimetry and calcium titration under conditions of low membrane occupancy showed that there was a strongly positive entropy change upon binding. For vesicles containing 25% phosphatidylserine at 0.15 m ionic strength, the free energy of binding was -53 kcal/mol protein, whereas the enthalpy of binding was -38 kcal/mol. Addition of 4 m urea decreased the free energy of binding by about 30% without denaturing the protein, suggesting that hydrophobic forces make a significant contribution to binding affinity. This was confirmed by mutagenesis studies that showed that binding affinity was modulated by the hydrophobicity of surface residues that are likely to enter the interfacial region upon protein-membrane binding. The change in free energy was quantitatively consistent with predictions from the Wimley-White scale of interfacial hydrophobicity. In contrast, binding affinity was not increased by making the protein surface more positively charged, nor decreased by making it more negatively charged, ruling out general ionic interactions as major contributors to binding affinity. The affinity of annexin V was the same regardless of the head group present on the anionic phospholipids tested (phosphatidylserine, phosphatidylglycerol, phosphatidylmethanol, and cardiolipin), ruling out specific interactions between the protein and non-phosphate moieties of the head group as a significant contributor to binding affinity. Analysis by fluorescence resonance energy transfer showed that multimers did not form on phosphatidylserine membranes at low occupancy, indicating that annexin-annexin interactions did not contribute to binding affinity. In summary, binding of annexin V to membranes is driven by both enthalpic and entropic forces. Dehydration of hydrophobic regions of the protein surface as they enter the interfacial region

  12. An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions.

    Directory of Open Access Journals (Sweden)

    Garima Tiwari

    Full Text Available Inhibitors of PDZ-peptide interactions have important implications in a variety of biological processes including treatment of cancer and Parkinson's disease. Even though experimental studies have reported characterization of peptidomimetic inhibitors of PDZ-peptide interactions, the binding modes for most of them have not been characterized by structural studies. In this study we have attempted to understand the structural basis of the small molecule-PDZ interactions by in silico analysis of the binding modes and binding affinities of a set of 38 small molecules with known K(i or K(d values for PDZ2 and PDZ3 domains of PSD-95 protein. These two PDZ domains show differential selectivity for these compounds despite having a high degree of sequence similarity and almost identical peptide binding pockets. Optimum binding modes for these ligands for PDZ2 and PDZ3 domains were identified by using a novel combination of semi-flexible docking and explicit solvent molecular dynamics (MD simulations. Analysis of the binding modes revealed most of the peptidomimectic ligands which had high K(i or K(d moved away from the peptide binding pocket, while ligands with high binding affinities remained in the peptide binding pocket. The differential specificities of the PDZ2 and PDZ3 domains primarily arise from differences in the conformation of the loop connecting βB and βC strands, because this loop interacts with the N-terminal chemical moieties of the ligands. We have also computed the MM/PBSA binding free energy values for these 38 compounds with both the PDZ domains from multiple 5 ns MD trajectories on each complex i.e. a total of 228 MD trajectories of 5 ns length each. Interestingly, computational binding free energies show good agreement with experimental binding free energies with a correlation coefficient of approximately 0.6. Thus our study demonstrates that combined use of docking and MD simulations can help in identification of potent inhibitors

  13. Binding interactions of pefloxacin mesylate with bovine lactoferrin and human serum albumin

    Institute of Scientific and Technical Information of China (English)

    FAN Ji-cai; CHEN Xiang; WANG Yun; FAN Cheng-ping; SHANG Zhi-cai

    2006-01-01

    The binding of pefloxacin mesylate (PFLX) to bovine lactoferrin (BLf) and human serum albumin (HSA) in dilute aqueous solution was studied using fluorescence spectra and absorbance spectra. The binding constant K and the binding sites n were obtained by fluorescence quenching method. The binding distance r and energy-transfer efficiency E between pefloxacin mesylate and bovine lactoferrin as well as human serum albumin were also obtained according to the mechanism of Forster-type dipole-dipole nonradiative energy-transfer. The effects of pefloxacin mesylate on the conformations of bovine lactoferrin and human serum albumin were also analyzed using synchronous fluorescence spectroscopy.

  14. Metal ion binding with carbon nanotubes and graphene: Effect of chirality and curvature

    Science.gov (United States)

    Umadevi, Deivasigamani; Sastry, G. Narahari

    2012-10-01

    First principles calculations have been used to comprehensively study the binding of a series alkali (Li+, Na+, K+) and alkaline earth (Be2+, Mg2+, Ca2+) metal ions with carbon nanotubes (CNTs) and graphene. It is interesting to note that the mono-cationic systems prefer binding to armchair CNTs over zigzag CNTs, while the preference for the di-cationic systems is exactly opposite. We have also observed significant changes in the HOMO-LUMO energy gap of the CNTs on metal ion binding and these results indicate that the fine tuning of energy gap of the CNTs can be effected through metal ion binding.

  15. Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead

    Science.gov (United States)

    Ropo, M.; Blum, V.; Baldauf, C.

    2016-11-01

    We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+. The underlying data set consists of more than 45,000 first-principles predicted conformers with relative energies up to ~4 eV (~400 kJ/mol). We show that only very few distinct backbone structures of isolated amino acids and their dipeptides emerge as lowest-energy conformers. The isolated amino acids predominantly adopt structures that involve an acidic proton shared between the carboxy and amino function. Dipeptides adopt one of two intramolecular-hydrogen bonded conformations C5 or . Upon complexation with a divalent cation, the accessible conformational space shrinks and intramolecular hydrogen bonding is prevented due to strong electrostatic interaction of backbone and side chain functional groups with cations. Clear correlations emerge from the binding energies of the six divalent ions with amino acids and dipeptides. Cd2+ and Hg2+ show the largest binding energies–a potential correlation with their known high acute toxicities. Ca2+ and Pb2+ reveal almost identical binding energies across the entire series of amino acids and dipeptides. This observation validates past indications that ion-mimicry of calcium and lead should play an important role in a toxicological context.

  16. Use of binding enthalpy to drive an allosteric transition.

    Science.gov (United States)

    Brown, Patrick H; Beckett, Dorothy

    2005-03-01

    The Escherichia coli biotin repressor is an allosteric DNA binding protein and is activated by the small molecule bio-5'-AMP. Binding of this small molecule promotes transcription repression complex assembly between the repressor and the biotin operator of the biotin biosynthetic operon. The ability of the adenylate to activate the assembly process reflects its effect on biotin repressor dimerization. Thus concomitant with small molecule binding the free energy of repressor dimerization becomes more favorable by approximately -4 kcal/mol. The structural, dynamic, and energetic changes in the repressor monomer that accompany allosteric activation are not known. In this work the thermodynamics of binding of four allosteric activators to the repressor have been characterized by isothermal titration calorimetry. While binding of two of the effectors results in relatively modest activation of the dimerization process, binding of the other two small molecules, including the physiological effector, leads to large changes in repressor dimerization energetics. Results of the calorimetric measurements indicate that strong effector binding is accompanied by an enthalpically costly transition in the protein. This transition is "paid for" by the enthalpy that would have otherwise been realized from the formation of noncovalent bonds between the ligand and repressor monomer.

  17. Cooperative binding: a multiple personality.

    Science.gov (United States)

    Martini, Johannes W R; Diambra, Luis; Habeck, Michael

    2016-06-01

    Cooperative binding has been described in many publications and has been related to or defined by several different properties of the binding behavior of the ligand to the target molecule. In addition to the commonly used Hill coefficient, other characteristics such as a sigmoidal shape of the overall titration curve in a linear plot, a change of ligand affinity of the other binding sites when a site of the target molecule becomes occupied, or complex roots of the binding polynomial have been used to define or to quantify cooperative binding. In this work, we analyze how the different properties are related in the most general model for binding curves based on the grand canonical partition function and present several examples which highlight differences between the cooperativity characterizing properties which are discussed. Our results mainly show that among the presented definitions there are not two which fully coincide. Moreover, this work poses the question whether it can make sense to distinguish between positive and negative cooperativity based on the macroscopic binding isotherm only. This article shall emphasize that scientists who investigate cooperative effects in biological systems could help avoiding misunderstandings by stating clearly which kind of cooperativity they discuss.

  18. Variations of nuclear binding with quark masses

    CERN Document Server

    Carrillo-Serrano, M E; Tsushima, K; Thomas, A W; Afnan, I R

    2012-01-01

    We investigate the variation with light quark mass of the mass of the nucleon as well as the masses of the mesons commonly used in a one-boson-exchange model of the nucleon-nucleon force. Care is taken to evaluate the meson mass shifts at the kinematic point relevant to that problem. Using these results, the corresponding changes in the energy of the 1 S0 anti-bound state, the binding energies of the deuteron, triton and selected finite nuclei are evaluated using a one-boson exchange model. The results are discussed in the context of possible corrections to the standard scenario for big bang nucleosynthesis in the case where, as suggested by recent observations of quasar absorption spectra, the quark masses may have changed over the age of the Universe.

  19. Evaluating the binding efficiency of pheromone binding protein with its natural ligand using molecular docking and fluorescence analysis

    Science.gov (United States)

    Ilayaraja, Renganathan; Rajkumar, Ramalingam; Rajesh, Durairaj; Muralidharan, Arumugam Ramachandran; Padmanabhan, Parasuraman; Archunan, Govindaraju

    2014-06-01

    Chemosignals play a crucial role in social and sexual communication among inter- and intra-species. Chemical cues are bound with protein that is present in the pheromones irrespective of sex are commonly called as pheromone binding protein (PBP). In rats, the pheromone compounds are bound with low molecular lipocalin protein α2u-globulin (α2u). We reported farnesol is a natural endogenous ligand (compound) present in rat preputial gland as a bound volatile compound. In the present study, an attempt has been made through computational method to evaluating the binding efficiency of α2u with the natural ligand (farnesol) and standard fluorescent molecule (2-naphthol). The docking analysis revealed that the binding energy of farnesol and 2-naphthol was almost equal and likely to share some binding pocket of protein. Further, to extrapolate the results generated through computational approach, the α2u protein was purified and subjected to fluorescence titration and binding assay. The results showed that the farnesol is replaced by 2-naphthol with high hydrophobicity of TYR120 in binding sites of α2u providing an acceptable dissociation constant indicating the binding efficiency of α2u. The obtained results are in corroboration with the data made through computational approach.

  20. Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead

    CERN Document Server

    Ropo, Matti; Baldauf, Carsten

    2016-01-01

    We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca$^{2+}$, Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data set consists of 45,892 first-principles predicted conformers with relative energies up to about 4 eV (about 400kJ/mol). We show that only very few distinct backbone structures of isolated amino acids and their dipeptides emerge as lowest-energy conformers. The isolated amino acids predominantly adopt structures that involve an acidic proton shared between the carboxy and amino function. Dipeptides adopt one of two intramolecular-hydrogen bonded conformations C$_5$ or equatorial C$_7$. Upon complexation with a divalent cation, the accessible conformational space shrinks and intramolecular hydrogen bonding is prevented due to strong electrostatic interaction of backbone and side chain functional groups with cations. Clear correlations emerge from the binding energies of the six divalent ...

  1. Probing ligand-binding modes and binding mechanisms of benzoxazole-based amide inhibitors with soluble epoxide hydrolase by molecular docking and molecular dynamics simulation.

    Science.gov (United States)

    Chen, Hang; Zhang, Ying; Li, Liang; Han, Ju-Guang

    2012-08-30

    Soluble epoxide hydrolase (sEH) has become a new therapeutic target for treating a variety of human diseases. The inhibition of human sEH hydrolase activity was studied by molecular docking and molecular dynamics (MD) simulation techniques. A set of six benzoxazole-based amide inhibitors binding to sEH has been studied through molecular docking, MD simulation, free energy calculations, and energy decomposition analysis. On the basis of molecular mechanics-generalized Born/surface area (MM-GB/SA) computation and normal-mode analysis (NMA), the obtained results indicate that the rank of calculated binding free energies (ΔΔGTOT) of these inhibitors is in excellent agreement with that of experimental bioactivity data (IC50). The correlation coefficient (r(2)) between the predicted ΔΔGTOT and IC50 is 0.88. van der Waals energies are the largest component of the total energies, and the entropy changes play an indispensable role in determining the ΔΔGTOT. Rational binding modes were discussed and determined by the docking results and binding free energies. The free energy decomposition of each residue reveals that the residue Trp334 dominates the most binding free energies among all residues and that the activities for these molecules to the sEH are not decided by hydrogen bonds or a certain residue but by the common effect of multiple side chains in the active site.

  2. The thermodynamic principles of ligand binding in chromatography and biology

    DEFF Research Database (Denmark)

    Mollerup, Jørgen

    2007-01-01

    . In the traditional adsorption models, the standard state Gibbs energy change of adsorption does not depend level of occupancy, but when it depends on the level of occupancy it gives rise to an adsorptive behaviour known as cooperativity. The binding of oxygen to haemoglobin is a well-known example from biology...

  3. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    and KCN, are selectively bound to the catalyst, providing exceptionally high enantioselectivities for kinetic resolutions, elimination reactions (fluoride base), and Strecker synthesis (cyanide nucleophile). Asymmetric cation-binding catalysis was recently expanded to silicon-based reagents, enabling...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...

  4. Predicting bioactive conformations and binding modes of macrocycles

    Science.gov (United States)

    Anighoro, Andrew; de la Vega de León, Antonio; Bajorath, Jürgen

    2016-10-01

    Macrocyclic compounds experience increasing interest in drug discovery. It is often thought that these large and chemically complex molecules provide promising candidates to address difficult targets and interfere with protein-protein interactions. From a computational viewpoint, these molecules are difficult to treat. For example, flexible docking of macrocyclic compounds is hindered by the limited ability of current docking approaches to optimize conformations of extended ring systems for pose prediction. Herein, we report predictions of bioactive conformations of macrocycles using conformational search and binding modes using docking. Conformational ensembles generated using specialized search technique of about 70 % of the tested macrocycles contained accurate bioactive conformations. However, these conformations were difficult to identify on the basis of conformational energies. Moreover, docking calculations with limited ligand flexibility starting from individual low energy conformations rarely yielded highly accurate binding modes. In about 40 % of the test cases, binding modes were approximated with reasonable accuracy. However, when conformational ensembles were subjected to rigid body docking, an increase in meaningful binding mode predictions to more than 50 % of the test cases was observed. Electrostatic effects did not contribute to these predictions in a positive or negative manner. Rather, achieving shape complementarity at macrocycle-target interfaces was a decisive factor. In summary, a combined computational protocol using pre-computed conformational ensembles of macrocycles as a starting point for docking shows promise in modeling binding modes of macrocyclic compounds.

  5. Alternative energies; Energies alternatives

    Energy Technology Data Exchange (ETDEWEB)

    Bonal, J.; Rossetti, P

    2007-07-01

    The earth took millions years to made the petroleum, the gas the coal and the uranium. Only a few centuries will be needed to exhaust these fossil fuels and some years to reach expensive prices. Will the wold continue on this way of energy compulsive consumption? The renewable energies and some citizen attitudes are sufficient to break this spiral. This book proposes to discuss these alternative energies. It shows that this attitude must be supported by the government. It takes stock on the more recent information concerning the renewable energies. it develops three main points: the electricity storage, the housing and the transports. (A.L.B.)

  6. Thermodynamic Exploration of Eosin-Lysozyme Binding: A Physical Chemistry and Biochemistry Laboratory Experiment

    Science.gov (United States)

    Huisman, Andrew J.; Hartsell, Lydia R.; Krueger, Brent P.; Pikaart, Michael J.

    2010-01-01

    We developed a modular pair of experiments for use in the undergraduate physical chemistry and biochemistry laboratories. Both experiments examine the thermodynamics of the binding of a small molecule, eosin Y, to the protein lysozyme. The assay for binding is the quenching of lysozyme fluorescence by eosin through resonant energy transfer. In…

  7. Intrinsically Disordered Energy Landscapes

    Science.gov (United States)

    Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

    2015-05-01

    Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium.

  8. Wind energies; Energies eoliennes

    Energy Technology Data Exchange (ETDEWEB)

    Martin, J.

    1997-01-01

    The main part of this study is focused on the wind turbine, including a full overview of turbine types, with in each case advantages, disadvantages and conditions of use. Subsidiary elements are mentioned, for support or energy conversion (into electricity, water pumping, heat generation). A glimpse is added to energy storage, and an economic balance is stroke. (D.L.)

  9. Cholesterol binding to ion channels

    Directory of Open Access Journals (Sweden)

    Irena eLevitan

    2014-02-01

    Full Text Available Numerous studies demonstrated that membrane cholesterol is a major regulator of ion channel function. The goal of this review is to discuss significant advances that have been recently achieved in elucidating the mechanisms responsible for cholesterol regulation of ion channels. The first major insight that comes from growing number of studies that based on the sterol specificity of cholesterol effects, show that several types of ion channels (nAChR, Kir, BK, TRPV are regulated by specific sterol-protein interactions. This conclusion is supported by demonstrating direct saturable binding of cholesterol to a bacterial Kir channel. The second major advance in the field is the identification of putative cholesterol binding sites in several types of ion channels. These include sites at locations associated with the well-known cholesterol binding motif CRAC and its reversed form CARC in nAChR, BK, and TRPV, as well as novel cholesterol binding regions in Kir channels. Notably, in the majority of these channels, cholesterol is suggested to interact mainly with hydrophobic residues in non-annular regions of the channels being embedded in between transmembrane protein helices. We also discuss how identification of putative cholesterol binding sites is an essential step to understand the mechanistic basis of cholesterol-induced channel regulation. Clearly, however, these are only the first few steps in obtaining a general understanding of cholesterol-ion channels interactions and their roles in cellular and organ functions.

  10. The prion protein binds thiamine.

    Science.gov (United States)

    Perez-Pineiro, Rolando; Bjorndahl, Trent C; Berjanskii, Mark V; Hau, David; Li, Li; Huang, Alan; Lee, Rose; Gibbs, Ebrima; Ladner, Carol; Dong, Ying Wei; Abera, Ashenafi; Cashman, Neil R; Wishart, David S

    2011-11-01

    Although highly conserved throughout evolution, the exact biological function of the prion protein is still unclear. In an effort to identify the potential biological functions of the prion protein we conducted a small-molecule screening assay using the Syrian hamster prion protein [shPrP(90-232)]. The screen was performed using a library of 149 water-soluble metabolites that are known to pass through the blood-brain barrier. Using a combination of 1D NMR, fluorescence quenching and surface plasmon resonance we identified thiamine (vitamin B1) as a specific prion ligand with a binding constant of ~60 μM. Subsequent studies showed that this interaction is evolutionarily conserved, with similar binding constants being seen for mouse, hamster and human prions. Various protein construct lengths, both with and without the unstructured N-terminal region in the presence and absence of copper, were examined. This indicates that the N-terminus has no influence on the protein's ability to interact with thiamine. In addition to thiamine, the more biologically abundant forms of vitamin B1 (thiamine monophosphate and thiamine diphosphate) were also found to bind the prion protein with similar affinity. Heteronuclear NMR experiments were used to determine thiamine's interaction site, which is located between helix 1 and the preceding loop. These data, in conjunction with computer-aided docking and molecular dynamics, were used to model the thiamine-binding pharmacophore and a comparison with other thiamine binding proteins was performed to reveal the common features of interaction.

  11. Enthalpy of captopril-angiotensin I-converting enzyme binding.

    Science.gov (United States)

    Ortiz-Salmerón, E; Barón, C; García-Fuentes, L

    1998-09-18

    High-sensitivity titration calorimetry is used to measure changes in enthalpy, heat capacity and protonation for the binding of captopril to the angiotensin I-converting enzyme (ACE; EC 3.4.15.1). The affinity of ACE to captopril is high and changes slightly with the pH, because the number of protons linked to binding is low. The determination of the enthalpy change at different pH values suggests that the protonated group in the captopril-ACE complex exhibits a heat protonation of approximately -30 kJ/mol. This value agrees with the protonation of an imidazole group. The residues which may become protonated in the complex could be two histidines existing in two active sites, which are joined to the amino acids coordinated to Zn2+. Calorimetric measurements indicate that captopril binds to two sites in the monomer of ACE, this binding being enthalpically unfavorable and being dominated by a large positive entropy change. Thus, binding is favored by both electrostatic and hydrophobic interactions. The temperature dependence of the free energy of binding deltaG degrees is weak because of the enthalpy-entropy compensation caused by a large heat capacity change, deltaCp =-4.3+/-0.1 kJ/K/mol of monomeric ACE. The strong favorable binding entropy and the negative deltaCp indicate both a large contribution to binding due to hydrophobic effects, which seem to originate from dehydration of the ligand-protein interface, and slight conformational changes in the vicinity of the active sites.

  12. Binding in light nuclei: Statistical NN uncertainties vs Computational accuracy

    CERN Document Server

    Perez, R Navarro; Amaro, J E; Arriola, E Ruiz

    2016-01-01

    We analyse the impact of the statistical uncertainties of the the nucleon-nucleon interaction, based on the Granada-2013 np-pp database, on the binding energies of the triton and the alpha particle using a bootstrap method, by solving the Faddeev equations for $^3$H and the Yakubovsky equations for $^4$He respectively. We check that in practice about 30 samples prove enough for a reliable error estimate. An extrapolation of the well fulfilled Tjon-line correlation predicts the experimental binding of the alpha particle within uncertainties.

  13. Effective-medium tight-binding model for silicon

    DEFF Research Database (Denmark)

    Stokbro, Kurt; Chetty, N.; Jacobsen, Karsten Wedel

    1994-01-01

    A method for calculating the total energy of Si systems, which is based on the effective-medium-theory concept of a reference system, is presented. Instead of calculating the energy of an atom in the system of interest, a reference system is introduced where the local surroundings are similar. Th...... and detailed description of the method is given together with test calculations of the energies of phonons, elastic constants, different structures, surfaces, and surface reconstructions. We compare the results to calculations using an empirical tight-binding scheme....

  14. Galectin-3-Binding and Metastasis

    Science.gov (United States)

    Nangia-Makker, Pratima; Balan, Vitaly; Raz, Avraham

    2013-01-01

    i. Summary Galectin-3 is a member of a family of carbohydrate-binding proteins. It is present in the nucleus, the cytoplasm and also extracellular matrix of many normal and neoplastic cell types. Arrays of reports show an upregulation of this protein in transformed and metastatic cell lines (1, 2). Moreover, in many human carcinomas, an increased expression of galectin-3 correlates with progressive tumor stages (3–6). Several lines of analysis have demonstrated that the galectins participate in cell-cell and cell-matrix interactions by recognizing and binding complimentary glycoconjugates and thereby play a crucial role in normal and pathological processes. Elevated expression of the protein is associated with an increased capacity for anchorage-independent growth, homotypic aggregation, and tumor cell lung colonization (7–9). In this chapter we describe the methods of purification of galectin-3 from transformed E. coli and some of the commonly used functional assays for analyzing galectin-3 binding. PMID:22674139

  15. Statistical Mechanics of Transcription-Factor Binding Site Discovery Using Hidden Markov Models.

    Science.gov (United States)

    Mehta, Pankaj; Schwab, David J; Sengupta, Anirvan M

    2011-04-01

    Hidden Markov Models (HMMs) are a commonly used tool for inference of transcription factor (TF) binding sites from DNA sequence data. We exploit the mathematical equivalence between HMMs for TF binding and the "inverse" statistical mechanics of hard rods in a one-dimensional disordered potential to investigate learning in HMMs. We derive analytic expressions for the Fisher information, a commonly employed measure of confidence in learned parameters, in the biologically relevant limit where the density of binding sites is low. We then use techniques from statistical mechanics to derive a scaling principle relating the specificity (binding energy) of a TF to the minimum amount of training data necessary to learn it.

  16. Computational Prediction of RNA-Binding Proteins and Binding Sites.

    Science.gov (United States)

    Si, Jingna; Cui, Jing; Cheng, Jin; Wu, Rongling

    2015-01-01

    Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein-RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  17. Computational Prediction of RNA-Binding Proteins and Binding Sites

    Directory of Open Access Journals (Sweden)

    Jingna Si

    2015-11-01

    Full Text Available Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs. Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  18. Binding of He{sub n}V clusters to α-Fe grain boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Tschopp, M. A., E-mail: mark.a.tschopp.civ@mail.mil [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States); Gao, F. [Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Solanki, K. N. [Arizona State University, Tempe, Arizona 85287 (United States)

    2014-06-21

    The objective of this research is to explore the formation/binding energetics and length scales associated with the interaction between He{sub n}V clusters and grain boundaries in bcc α-Fe. In this work, we calculated formation/binding energies for 1–8 He atoms in a monovacancy at all potential grain boundary (GB) sites within 15 Å of the ten grain boundaries selected (122106 simulations total). The present results provide detailed information about the interaction energies and length scales of 1–8 He atoms with grain boundaries for the structures examined. A number of interesting new findings emerge from the present study. First, the Σ3(112) “twin” GB has significantly lower binding energies for all He{sub n}V clusters than all other boundaries in this study. For all grain boundary sites, the effect of the local environment surrounding each site on the He{sub n}V formation and binding energies decreases with an increasing number of He atoms in the He{sub n}V cluster. Based on the calculated dataset, we formulated a model to capture the evolution of the formation and binding energy of He{sub n}V clusters as a function of distance from the GB center, utilizing only constants related to the maximum binding energy and the length scale.

  19. Synthetic heparin-binding growth factor analogs

    Science.gov (United States)

    Pena, Louis A.; Zamora, Paul; Lin, Xinhua; Glass, John D.

    2007-01-23

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain that binds a heparin-binding growth factor receptor, covalently bound to a hydrophobic linker, which is in turn covalently bound to a non-signaling peptide that includes a heparin-binding domain. The synthetic heparin-binding growth factor analogs are useful as soluble biologics or as surface coatings for medical devices.

  20. Energy Handbook; Energy Vademecum

    Energy Technology Data Exchange (ETDEWEB)

    Israels, E.; Stofberg, F.

    2010-05-15

    This is the third and revised print of the Handbook energy-conscious designing of new dwellings. The handbook addresses the latest developments in the field of developing, designing and realizing of new dwellings. [Dutch] Dit is een derde en sterk herziene druk van het 'Vademecum energiebewust ontwerpen van nieuwbouwwoningen', dat in 1992 verscheen. In het 'EnergieVademecum' komen de nieuwste ontwikkelingen op het gebied van energiebewust ontwikkelen, ontwerpen en realiseren van nieuwbouwwoningen aan bod.

  1. Binding of TNT to amplifying fluorescent polymers: an ab initio and molecular dynamics study.

    Science.gov (United States)

    Enlow, Mark A

    2012-03-01

    Molecular modeling techniques were employed to study the interaction of trinitrotoluene with an amplifying fluorescent polymer used in explosive sensor devices. The pentiptycene moiety present in these polymers appears to be the most energetically favorable binding site for trinitrotoluene. Surface features of the polymer suggest that the small cavity feature of the pentiptycene moiety may be more available for binding to analyte compounds due to steric crowding about the large cavity. Binding energies between model binding sites of the polymer and various analyte compounds were more rigorously estimated by semiempirical and ab initio techniques. Binding energies were found to be largest with trinitrotoluene and other nitroaromatic compounds. Electrostatic and π-stacking interactions between trinitrotoluene and the model host were investigated by studying a series of modified host compounds.

  2. Cellulose binding domain fusion proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  3. Metal ion enhanced binding of AMD3100 to Asp262 in the CXCR4 receptor

    DEFF Research Database (Denmark)

    Gerlach, Lars Ole; Jakobsen, Janus S; Jensen, Kasper P;

    2003-01-01

    +), Zn(2+), or Ni(2+) into the cyclam rings of the compound. The rank order of the transition metal ions correlated with the calculated binding energy between free acetate and the metal ions coordinated in a cyclam ring. Construction of AMD3100 substituted with only a single Cu(2+) or Ni(2+) ion...... demonstrated that the increase in binding affinity of the metal ion substituted bicyclam is achieved through an enhanced interaction of just one of the ring systems. Mutational analysis of potential metal ion binding residues in the main ligand binding crevice of the CXCR4 receptor showed that although binding...... of the bicyclam is dependent on both Asp(171) and Asp(262), the enhancing effect of the metal ion was selectively eliminated by substitution of Asp(262) located at the extracellular end of TM-VI. It is concluded that the increased binding affinity of the metal ion substituted AMD3100 is obtained through enhanced...

  4. Thermodynamic parameters for binding of fatty acids to human serum albumin

    DEFF Research Database (Denmark)

    Pedersen, A O; Honoré, B; Brodersen, R

    1990-01-01

    Binding of laurate and myristate anions to human serum albumin has been studied over a range of temperatures, 5-37 degrees C, at pH 7.4. The binding curves indicate that the strength of binding of the first few molecules of fatty acid to albumin (r less than 5) decreases with increasing temperature...... constant, it was possible to calculate values for the changes in enthalpy and entropy during the initial binding step. For the medium-chain fatty acids, laurate and myristate, binding of the first molecule to albumin appeared to be enthalpic, with a tendency to an increasing contribution of entropy...... to binding energy with increasing chain length of the fatty acid. Udgivelsesdato: 1990-Jul-5...

  5. Protein binding assay for hyaluronate

    Energy Technology Data Exchange (ETDEWEB)

    Lacy, B.E.; Underhill, C.B.

    1986-11-01

    A relatively quick and simple assay for hyaluronate was developed using the specific binding protein, hyaluronectin. The hyaluronectin was obtained by homogenizing the brains of Sprague-Dawley rats, and then centrifuging the homogenate. The resulting supernatant was used as a source of crude hyaluronectin. In the binding assay, the hyaluronectin was mixed with (/sup 3/H)hyaluronate, followed by an equal volume of saturated (NH/sub 4/)/sub 2/SO/sub 4/, which precipitated the hyaluronectin and any (/sup 3/H)hyaluronate associated with it, but left free (/sup 3/H)hyaluronate in solution. The mixture was then centrifuged, and the amount of bound (/sup 3/H)hyaluronate in the precipitate was determined. Using this assay, the authors found that hyaluronectin specifically bound hyaluronate, since other glycosaminoglycans failed to compete for the binding protein. In addition, the interaction between hyaluronectin and hyaluronate was of relatively high affinity, and the size of the hyaluronate did not appear to substantially alter the amount of binding. To determine the amount of hyaluronate in an unknown sample, they used a competition assay in which the binding of a set amount of (/sup 3/H)hyaluronate was blocked by the addition of unlabeled hyaluronate. By comparing the degree of competition of the unknown samples with that of known amounts of hyaluronate, it was possible to determine the amount of hyaluronate in the unknowns. They have found that this method is sensitive to 1 ..mu..g or less of hyaluronate, and is unaffected by the presence of proteins.

  6. Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study.

    Science.gov (United States)

    Shao, Qing; Hall, Carol K

    2016-08-09

    A better understanding of the binding preference of amino acids for gold nanoparticles of different diameters could aid in the design of peptides that bind specifically to nanoparticles of a given diameter. Here we identify the binding preference of 19 natural amino acids for three gold nanoparticles with diameters of 1.0, 2.0, and 4.0 nm, and investigate the mechanisms that govern these preferences. We calculate potentials of mean force between 36 entities (19 amino acids and 17 side chains) and the three gold nanoparticles in explicit water using well-tempered metadynamics simulations. Comparing these potentials of mean force determines the amino acids' nanoparticle binding preferences and if these preferences are controlled by the backbone, the side chain, or both. Twelve amino acids prefer to bind to the 4.0 nm gold nanoparticle, and seven prefer to bind to the 2.0 nm one. We also use atomistic molecular dynamics simulations to investigate how water molecules near the nanoparticle influence the binding of the amino acids. The solvation shells of the larger nanoparticles have higher water densities than those of the smaller nanoparticles while the orientation distributions of the water molecules in the shells of all three nanoparticles are similar. The nanoparticle preferences of the amino acids depend on whether their binding free energy is determined mainly by their ability to replace or to reorient water molecules in the nanoparticle solvation shell. The amino acids whose binding free energy depends mainly on the replacement of water molecules are likely to prefer to bind to the largest nanoparticle and tend to have relatively simple side chain structures. Those whose binding free energy depends mainly on their ability to reorient water molecules prefer a smaller nanoparticle and tend to have more complex side chain structures.

  7. Specific binding of benzodiazepines to human breast cancer cell lines.

    Science.gov (United States)

    Beinlich, A; Strohmeier, R; Kaufmann, M; Kuhl, H

    1999-01-01

    Binding of [3H]Ro5-4864, a peripheral benzodiazepine receptor (PBR) agonist, to BT-20 human, estrogen- (ER) and progesterone- (PR) receptor negative breast cancer cells was characterized. It was found to be specific, dose-dependent and saturable with a single population of binding sites. Dissociation constant (K(D)) was 8.5 nM, maximal binding capacity (Bmax) 339 fM/10(6) cells. Ro5-4864 (IC50 17.3 nM) and PK 11195 (IC50 12.3 nM) were able to compete with [3H]Ro5-4864 for binding, indicating specificity of interaction with PBR. Diazepam was able to displace [3H]Ro5-4864 from binding only at high concentrations (>1 microM), while ODN did not compete for PBR binding. Thymidine-uptake assay showed a biphasic response of cell proliferation. While low concentrations (100 nM) of Ro5-4864, PK 11195 and diazepam increased cell growth by 10 to 20%, higher concentrations (10-100 microM) significantly inhibited cell proliferation. PK 11195, a potent PBR ligand, was able to attenuate growth of BT-20 cells stimulated by 100 nM Ro5-4864 and to reverse growth reduction caused by 1 and 10 microM Ro5-4864, but not by 50 microM and 100 microM. This indicates that the antimitotic activity of higher concentrations of Ro5-4864 is independent of PBR binding. It is suggested, that PBR are involved in growth regulation of certain human breast cancer cell lines, possibly by supplying proliferating cells with energy, as their endogenous ligand is a polypeptide transporting Acyl-CoA.

  8. How Native and Alien Metal Cations Bind ATP: Implications for Lithium as a Therapeutic Agent

    Science.gov (United States)

    Dudev, Todor; Grauffel, Cédric; Lim, Carmay

    2017-01-01

    Adenosine triphosphate (ATP), the major energy currency of the cell, exists in solution mostly as ATP-Mg. Recent experiments suggest that Mg2+ interacts with the highly charged ATP triphosphate group and Li+ can co-bind with the native Mg2+ to form ATP-Mg-Li and modulate the neuronal purine receptor response. However, it is unclear how the negatively charged ATP triphosphate group binds Mg2+ and Li+ (i.e. which phosphate group(s) bind Mg2+/Li+) and how the ATP solution conformation depends on the type of metal cation and the metal-binding mode. Here, we reveal the preferred ATP-binding mode of Mg2+/Li+ alone and combined: Mg2+ prefers to bind ATP tridentately to each of the three phosphate groups, but Li+ prefers to bind bidentately to the terminal two phosphates. We show that the solution ATP conformation depends on the cation and its binding site/mode, but it does not change significantly when Li+ binds to Mg2+-loaded ATP. Hence, ATP-Mg-Li, like Mg2+-ATP, can fit in the ATP-binding site of the host enzyme/receptor, activating specific signaling pathways. PMID:28195155

  9. How Native and Alien Metal Cations Bind ATP: Implications for Lithium as a Therapeutic Agent

    Science.gov (United States)

    Dudev, Todor; Grauffel, Cédric; Lim, Carmay

    2017-02-01

    Adenosine triphosphate (ATP), the major energy currency of the cell, exists in solution mostly as ATP-Mg. Recent experiments suggest that Mg2+ interacts with the highly charged ATP triphosphate group and Li+ can co-bind with the native Mg2+ to form ATP-Mg-Li and modulate the neuronal purine receptor response. However, it is unclear how the negatively charged ATP triphosphate group binds Mg2+ and Li+ (i.e. which phosphate group(s) bind Mg2+/Li+) and how the ATP solution conformation depends on the type of metal cation and the metal-binding mode. Here, we reveal the preferred ATP-binding mode of Mg2+/Li+ alone and combined: Mg2+ prefers to bind ATP tridentately to each of the three phosphate groups, but Li+ prefers to bind bidentately to the terminal two phosphates. We show that the solution ATP conformation depends on the cation and its binding site/mode, but it does not change significantly when Li+ binds to Mg2+-loaded ATP. Hence, ATP-Mg-Li, like Mg2+-ATP, can fit in the ATP-binding site of the host enzyme/receptor, activating specific signaling pathways.

  10. Capacitance-modulated transistor detects odorant binding protein chiral interactions

    Science.gov (United States)

    Mulla, Mohammad Yusuf; Tuccori, Elena; Magliulo, Maria; Lattanzi, Gianluca; Palazzo, Gerardo; Persaud, Krishna; Torsi, Luisa

    2015-01-01

    Peripheral events in olfaction involve odorant binding proteins (OBPs) whose role in the recognition of different volatile chemicals is yet unclear. Here we report on the sensitive and quantitative measurement of the weak interactions associated with neutral enantiomers differentially binding to OBPs immobilized through a self-assembled monolayer to the gate of an organic bio-electronic transistor. The transduction is remarkably sensitive as the transistor output current is governed by the small capacitance of the protein layer undergoing minute changes as the ligand-protein complex is formed. Accurate determination of the free-energy balances and of the capacitance changes associated with the binding process allows derivation of the free-energy components as well as of the occurrence of conformational events associated with OBP ligand binding. Capacitance-modulated transistors open a new pathway for the study of ultra-weak molecular interactions in surface-bound protein-ligand complexes through an approach that combines bio-chemical and electronic thermodynamic parameters.

  11. Binding of beta-scorpion toxin: a physicochemical study.

    Science.gov (United States)

    Jover, E; Bablito, J; Couraud, F

    1984-03-13

    The binding to rat brain synaptosomes of a beta-scorpion toxin, i.e., toxin II of Centruroides suffusus suffusus (Css II), was studied as a function of pH, temperature, and concentration of some monovalent and divalent cations. At 10 degrees C and pH 6.0, the specific binding of 125I-labeled Css II corresponds to a single class of noninteracting high-affinity binding sites (KD = 0.18 nM) with a capacity (4.2 pmol/mg of protein) that is almost identical with that generally accepted for saxitoxin. The equilibrium dissociation constant of beta-scorpion toxin is pH independent, but the maximum binding capacity is reduced with increasing pH. Li+, guanidinium, Ca2+, Mg2+, and Mn2+ modified the apparent KD of the 125I-labeled Css II toxin. The equilibrium dissociation constant varies markedly with the temperature. The van't Hoff plot of the data is curvilinear, corresponding to a standard free-energy change associated with an entropy-driven process. The association rate constant also varies considerably with the temperature whereas the Arrhenius plot is linear between 1 and 30 degrees C. The energy of activation determined from these data is 17.6 kcal/mol. These results support the hypothesis that a cluster of nonpolar amino acid residues present on one face of the molecule is involved in the toxin-receptor interaction.

  12. Energy options?; Energie opties?

    Energy Technology Data Exchange (ETDEWEB)

    Van Sark, W. (ed.)

    2006-05-15

    March 2006 the so-called Options Document was published by the Energy research Centre of the Netherlands (ECN) and the Netherlands Environmental Assessment Agency (MNP). The document is an overview of technical options to reduce energy consumption and emission of greenhouse gases up to 2020. Next to a brief summary of the document a few reactions and comments on the contents of the document are given. [Dutch] Maart 2006 publiceerde het Energieonderzoek Centrum Nederland (ECN) en het Milieu- en Natuurplanbureau (MNP) het zogenaamde Optiedocument energie en emissies 2010-2020. Daarin wordt een overzicht gegeven van de technische mogelijkheden voor vermindering van het energieverbruik en de uitstoot van broeikasgassen en luchtverontreinigende stoffen tot 2020. Naast een korte samenvatting van het document worden enkele reacties gegeven op de inhoud.

  13. Energy Technology.

    Science.gov (United States)

    Eaton, William W.

    Reviewed are technological problems faced in energy production including locating, recovering, developing, storing, and distributing energy in clean, convenient, economical, and environmentally satisfactory manners. The energy resources of coal, oil, natural gas, hydroelectric power, nuclear energy, solar energy, geothermal energy, winds, tides,…

  14. Binding Blocks: building the Universe one nucleus at the time

    CERN Document Server

    Diget, C Aa; Leech, K; Haylett, T; Lock, S; Sanders, T; Shelley, M; Willett, H V; Keegans, J; Sinclair, L; Simpson, E C

    2016-01-01

    We present a new teaching and outreach activity based around the construction of a three-dimensional chart of isotopes using LEGO$^{\\copyright}$ bricks. The activity, \\emph{Binding Blocks}, demonstrates nuclear and astrophysical processes through a seven-meter chart of all nuclear isotopes, built from over 26,000 LEGO$^{\\copyright}$ bricks. It integrates A-level and GCSE curricula across areas of nuclear physics, astrophysics, and chemistry, including: nuclear decays (through the colours in the chart); nuclear binding energy (through tower heights); production of chemical elements in the cosmos; fusion processes in stars and fusion energy on Earth; as well as links to medical physics, particularly diagnostics and radiotherapy.

  15. Binding blocks: building the Universe one nucleus at a time

    Science.gov (United States)

    Diget, C. Aa; Pastore, A.; Leech, K.; Haylett, T.; Lock, S.; Sanders, T.; Shelley, M.; Willett, H. V.; Keegans, J.; Sinclair, L.; Simpson, E. C.; the Binding Blocks Collaboration

    2017-03-01

    We present a new teaching and outreach activity based around the construction of a three-dimensional chart of isotopes using \\text{LEG}{{\\text{O}}\\circledR} bricks5. The activity, binding blocks, demonstrates nuclear and astrophysical processes through a seven-meter chart of all nuclear isotopes, built from over 26 000 \\text{LEG}{{\\text{O}}\\circledR} bricks. It integrates A-Level and GCSE curricula across areas of nuclear physics, astrophysics, and chemistry, including: nuclear decays (through the colours in the chart); nuclear binding energy (through tower heights); production of chemical elements in the cosmos; fusion processes in stars and fusion energy on Earth; as well as links to medical physics, particularly diagnostics and radiotherapy.

  16. FRACTURE FEATURES OF METAL BINDING WHEN DIAMOND-SPARK GRINDING

    Directory of Open Access Journals (Sweden)

    Yury GUTSALENKO

    2012-05-01

    Full Text Available The hypothesis of the influence of binding energy of metal on the processes of destruction and mass transfer at high-speed machining is considered. Some nonconventional processes of cleaning of intergranularity spaces from waste products at diamond-spark grinding are explained, the approach to assessment of metal resistance in these processes is proposed and eo ipso modern conception of processes in chip formation zone under condition of electric discharge effect is supplemented

  17. Human plasminogen binding protein tetranectin

    DEFF Research Database (Denmark)

    Kastrup, J S; Rasmussen, H; Nielsen, B B;

    1997-01-01

    The recombinant human plasminogen binding protein tetranectin (TN) and the C-type lectin CRD of this protein (TN3) have been crystallized. TN3 crystallizes in the tetragonal space group P4(2)2(1)2 with cell dimensions a = b = 64.0, c = 75.7 A and with one molecule per asymmetric unit. The crystals...... to at least 2.5 A. A full data set has been collected to 3.0 A. The asymmetric unit contains one monomer of TN. Molecular replacement solutions for TN3 and TN have been obtained using the structure of the C-type lectin CRD of rat mannose-binding protein as search model. The rhombohedral space group indicates...

  18. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen;

    2012-01-01

    Proteomics and high throughput analysis for systems biology can benefit significantly from solid-phase chemical tools for affinity pull-down of proteins from complex mixtures. Here we report the application of solid-phase synthesis of phosphopeptides for pull-down and analysis of the affinity...... around the phosphorylated residue are important for the binding affinity of ILKAP. We conclude that solid-phase affinity pull-down of proteins from complex mixtures can be applied in phosphoproteomics and systems biology....

  19. Analytical models of calcium binding in a calcium channel

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jinn-Liang [Department of Applied Mathematics, National Hsinchu University of Education, Hsinchu 300, Taiwan (China); Eisenberg, Bob [Department of Molecular Biophysics and Physiology, Rush University, Chicago, Illinois 60612 (United States)

    2014-08-21

    The anomalous mole fraction effect of L-type calcium channels is analyzed using a Fermi like distribution with the experimental data of Almers and McCleskey [J. Physiol. 353, 585 (1984)] and the atomic resolution model of Lipkind and Fozzard [Biochemistry 40, 6786 (2001)] of the selectivity filter of the channel. Much of the analysis is algebraic, independent of differential equations. The Fermi distribution is derived from the configuration entropy of ions and water molecules with different sizes, different valences, and interstitial voids between particles. It allows us to calculate potentials and distances (between the binding ion and the oxygen ions of the glutamate side chains) directly from the experimental data using algebraic formulas. The spatial resolution of these results is comparable with those of molecular models, but of course the accuracy is no better than that implied by the experimental data. The glutamate side chains in our model are flexible enough to accommodate different types of binding ions in different bath conditions. The binding curves of Na{sup +} and Ca{sup 2+} for [CaCl{sub 2}] ranging from 10{sup −8} to 10{sup −2} M with a fixed 32 mM background [NaCl] are shown to agree with published Monte Carlo simulations. The Poisson-Fermi differential equation—that includes both steric and correlation effects—is then used to obtain the spatial profiles of energy, concentration, and dielectric coefficient from the solvent region to the filter. The energy profiles of ions are shown to depend sensitively on the steric energy that is not taken into account in the classical rate theory. We improve the rate theory by introducing a steric energy that lumps the effects of excluded volumes of all ions and water molecules and empty spaces between particles created by Lennard-Jones type and electrostatic forces. We show that the energy landscape varies significantly with bath concentrations. The energy landscape is not constant.

  20. Investigation of three flavonoids binding to bovine serum albumin using molecular fluorescence technique

    Energy Technology Data Exchange (ETDEWEB)

    Bi Shuyun, E-mail: sy_bi@sina.com [College of Chemistry, Changchun Normal University, Changchun 130032 (China); Yan Lili; Pang Bo; Wang Yu [College of Chemistry, Changchun Normal University, Changchun 130032 (China)

    2012-01-15

    The three flavonoids including naringenin, hesperetin and apigenin binding to bovine serum albumin (BSA) at pH 7.4 was studied by fluorescence quenching, synchronous fluorescence and UV-vis absorption spectroscopic techniques. The results obtained revealed that naringenin, hesperetin and apigenin strongly quenched the intrinsic fluorescence of BSA. The Stern-Volmer curves suggested that these quenching processes were all static quenching processes. At 291 K, the value and the order of the binding constant were K{sub A{sub (naringenin)}}=4.08x10{sup 4}binding force between the flavonoid and BSA was hydrophobic and electrostatic force. According to the Foerster theory of non-radiation energy transfer, the binding distances (r{sub 0}) were obtained as 3.36, 3.47 and 3.30 nm for naringenin-BSA, hesperetin-BSA and apigenin-BSA, respectively. The effect of some common ions such as Fe{sup 3+}, Cu{sup 2+}, Mg{sup 2+}, Mn{sup 2+}, Zn{sup 2+} and Ca{sup 2+} on the binding was also studied in detail. The competition binding was also performed. The apparent binding constant (K'{sub A}) obtained suggested that one flavonoid had an obvious effect on the binding of another flavonoid to protein when they coexisted in BSA solution. - Highlights: > Quenchings of BSA fluorescence by the flavonoids was all static quenchings. > Synchronous fluorescence was applied to study the structural change of BSA. > Binding constant, binding site and binding force were determined. > Competition binding experiments were performed. > One flavonoid had an obvious effect on the binding of another one to BSA.

  1. Determination of binding specificity between receptors and probes covering HIV-1 gp41 NHR in fluorescence resonance energy transfer assay%HIV-1gp41NHR序列靶点专一性的荧光共振能转移测定

    Institute of Scientific and Technical Information of China (English)

    王昆; 郑保华; 蔡利锋; 刘克良; 李艳妮

    2013-01-01

    目的 确定并利用荧光共振能转移法(FRET)对以HIV-1 gp41 N端七联重复序列(NHR)为靶点的融合抑制剂进行筛选和作用机制研究.方法 FRET采用金属络合物多肽技术设计针对不同结合位点、结合强度可调、涵盖全部NHR序列的靶点和探针,对HIV融合抑制剂进行高通量筛选.由于HIV在进行膜融合时其gp41的N端NHR和C端CHR可形成稳定的六螺旋结构,因此,利用圆二色谱仪对FRET所使用的靶点/探针对的结合强度进行验证,确定对应的靶点/探针对可形成稳定的六螺旋结构;同时,借助细胞活性测试测定抑制剂的活性,验证FRET是否可用于筛选以HIV-1 gp41 NHR为靶点的抑制剂.结果与结论 FRET中使用的靶点/探针均可形成螺旋度较高的六螺旋结构,其中Fe(Env2.0)3/CP2及Fe(Env5.0)3/CP5形成的α螺旋度分别高达89.6%和84.7%.FRET所使用的靶点/探针对专一性强、结合作用强,可用于进行HIV-1融合抑制剂的筛选和机制研究.%Objective To identify and optimize a fluorescence resonance energy transfer ( FRET )-based assay to screen fusion inhibitors which target HIV-1 gp41 N-terminal heptad repeats( NHR ) and to study their mechanisms. Methods The FRET assay using metallopeptide technology was applied to detect HIV fusion inhibitors in a high-throughput mode, by which receptors and probes were designed to cover all the possible NHR binding sites with flexible binding affinities. The assay biochemically represented a stable fusion-active conformation of the envelope protein gp41 of HIV-1, which was a six-helix bundle formed by NHR and C-terminal heptad repeat ( CHR ) in the process of virus-cell membrane fusion. The six-helix bundle formed by an NHR-derived receptor and CHR-derived probe was characterized by circular dichroism to verify the effective receptor/probe pair, and the FRET assay was verified by comparing the result of the assay with a well-established cell-cell fusion assay using known

  2. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  3. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  4. Energy intermittency

    CERN Document Server

    Sorensen, Bent

    2014-01-01

    The first book to consider intermittency as a key point of an energy system, Energy Intermittency describes different levels of variability for traditional and renewable energy sources, presenting detailed solutions for handling energy intermittency through trade, collaboration, demand management, and active energy storage. Addressing energy supply intermittency systematically, this practical text:Analyzes typical time-distributions and intervals between episodes of demand-supply mismatch and explores their dependence on system layouts and energy source characteristicsSimulates scenarios regar

  5. DAPI binding to the DNA minor groove: a continuum solvent analysis.

    Science.gov (United States)

    De Castro, L F Pineda; Zacharias, M

    2002-01-01

    A continuum solvent model based on the generalized Born (GB) or finite-difference Poisson-Boltzmann (FDPB) approaches has been employed to compare the binding of 4'-6-diamidine-2-phenyl indole (DAPI) to the minor groove of various DNA sequences. Qualitative agreement between the results of GB and FDPB approaches as well as between calculated and experimentally observed trends regarding the sequence specificity of DAPI binding to B-DNA was obtained. Calculated binding energies were decomposed into various contributions to solvation and DNA-ligand interaction. DNA conformational adaptation was found to make a favorable contribution to the calculated total interaction energy but did not change the DAPI binding affinity ranking of different DNA sequences. The calculations indicate that closed complex formation is mainly driven by nonpolar contributions and was found to be disfavored electrostatically due to a desolvation penalty that outbalances the attractive Coulomb interaction. The calculated penalty was larger for DAPI binding to GC-rich sequences compared with AT-rich target sequences and generally larger for the FDPB vs the GB continuum model. A radial interaction profile for DAPI at different distances from the DNA minor groove revealed an electrostatic energy minimum a few Angstroms farther away from the closed binding geometry. The calculated electrostatic interaction up to this distance is attractive and it may stabilize a nonspecific binding arrangement.

  6. Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics.

    Science.gov (United States)

    Henriksen, Niel M; Fenley, Andrew T; Gilson, Michael K

    2015-09-08

    We present a strategy for carrying out high-precision calculations of binding free energy and binding enthalpy values from molecular dynamics simulations with explicit solvent. The approach is used to calculate the thermodynamic profiles for binding of nine small molecule guests to either the cucurbit[7]uril (CB7) or β-cyclodextrin (βCD) host. For these systems, calculations using commodity hardware can yield binding free energy and binding enthalpy values with a precision of ∼0.5 kcal/mol (95% CI) in a matter of days. Crucially, the self-consistency of the approach is established by calculating the binding enthalpy directly, via end point potential energy calculations, and indirectly, via the temperature dependence of the binding free energy, i.e., by the van't Hoff equation. Excellent agreement between the direct and van't Hoff methods is demonstrated for both host-guest systems and an ion-pair model system for which particularly well-converged results are attainable. Additionally, we find that hydrogen mass repartitioning allows marked acceleration of the calculations with no discernible cost in precision or accuracy. Finally, we provide guidance for accurately assessing numerical uncertainty of the results in settings where complex correlations in the time series can pose challenges to statistical analysis. The routine nature and high precision of these binding calculations opens the possibility of including measured binding thermodynamics as target data in force field optimization so that simulations may be used to reliably interpret experimental data and guide molecular design.

  7. The nuclear symmetry energy

    Science.gov (United States)

    Baldo, M.; Burgio, G. F.

    2016-11-01

    The nuclear symmetry energy characterizes the variation of the binding energy as the neutron to proton ratio of a nuclear system is varied. This is one of the most important features of nuclear physics in general, since it is just related to the two component nature of the nuclear systems. As such it is one of the most relevant physical parameters that affect the physics of many phenomena and nuclear processes. This review paper presents a survey of the role and relevance of the nuclear symmetry energy in different fields of research and of the accuracy of its determination from the phenomenology and from the microscopic many-body theory. In recent years, a great interest was devoted not only to the Nuclear Matter symmetry energy at saturation density but also to its whole density dependence, which is an essential ingredient for our understanding of many phenomena. We analyze the nuclear symmetry energy in different realms of nuclear physics and astrophysics. In particular we consider the nuclear symmetry energy in relation to nuclear structure, astrophysics of Neutron Stars and supernovae, and heavy ion collision experiments, trying to elucidate the connections of these different fields on the basis of the symmetry energy peculiarities. The interplay between experimental and observational data and theoretical developments is stressed. The expected future developments and improvements are schematically addressed, together with most demanded experimental and theoretical advances for the next few years.

  8. Engineering RNA-binding proteins for biology

    OpenAIRE

    Chen,Yu; Varani, Gabriele

    2013-01-01

    RNA-binding proteins play essential roles in the regulation of gene expression. Many have modular structures and combine relatively few common domains in various arrangements to recognize RNA sequences and/or structures. Recent progress in engineering the specificity of the PUF class RNA-binding proteins has shown that RNA-binding domains may be combined with various effector or functional domains to regulate the metabolism of targeted RNAs. Designer RNA-binding proteins with tailored sequenc...

  9. Energy sustainability through green energy

    CERN Document Server

    Sharma, Atul

    2015-01-01

    This book shares the latest developments and advances in materials and processes involved in the energy generation, transmission, distribution and storage. Chapters are written by researchers in the energy and materials field. Topics include, but are not limited to, energy from biomass, bio-gas and bio-fuels; solar, wind, geothermal, hydro power, wave energy; energy-transmission, distribution and storage; energy-efficient lighting buildings; energy sustainability; hydrogen and fuel cells; energy policy for new and renewable energy technologies and education for sustainable energy development

  10. Mode of encapsulation of linezolid by β-cyclodextrin and its role in bovine serum albumin binding.

    Science.gov (United States)

    Natesan, Sudha; Sowrirajan, Chandrasekaran; Yousuf, Sameena; Enoch, Israel V M V

    2015-01-22

    We describe, in this article, the associative interaction between Linezolid and β-Cyclodextrin, and the influence of β-Cyclodextrin on Linezolid's binding to Bovine serum albumin. β-Cyclodextrin forms a 1:1 inclusion complex with Linezolid, with a binding constant value of 3.51×10(2)M(-1). The binding is studied using ultraviolet-visible absorption, fluorescence, nuclear magnetic resonance, and rotating-frame overhauser effect spectroscopic techniques. The amide substituent on the oxazolidinone ring of Linezolid is involved in its binding to β-Cyclodextrin. The binding of the Linezolid to bovine serum albumin, in the absence and the presence of β-Cyclodextrin, is studied by analyzing the fluorescence quenching and Förster resonance energy transfer. The Stern-Volmer quenching constant, the binding constant, and energy transfer occurring on the interaction of the Linezolid with BSA are found to be smaller in the presence of β-Cyclodextrin than in water.

  11. Renewable energy.

    Science.gov (United States)

    Destouni, Georgia; Frank, Harry

    2010-01-01

    The Energy Committee of the Royal Swedish Academy of Sciences has in a series of projects gathered information and knowledge on renewable energy from various sources, both within and outside the academic world. In this article, we synthesize and summarize some of the main points on renewable energy from the various Energy Committee projects and the Committee's Energy 2050 symposium, regarding energy from water and wind, bioenergy, and solar energy. We further summarize the Energy Committee's scenario estimates of future renewable energy contributions to the global energy system, and other presentations given at the Energy 2050 symposium. In general, international coordination and investment in energy research and development is crucial to enable future reliance on renewable energy sources with minimal fossil fuel use.

  12. Energy resources

    CERN Document Server

    Simon, Andrew L

    1975-01-01

    Energy Resources mainly focuses on energy, including its definition, historical perspective, sources, utilization, and conservation. This text first explains what energy is and what its uses are. This book then explains coal, oil, and natural gas, which are some of the common energy sources used by various industries. Other energy sources such as wind, solar, geothermal, water, and nuclear energy sources are also tackled. This text also looks into fusion energy and techniques of energy conversion. This book concludes by explaining the energy allocation and utilization crisis. This publ

  13. Feature-Based Binding and Phase Theory

    Science.gov (United States)

    Antonenko, Andrei

    2012-01-01

    Current theories of binding cannot provide a uniform account for many facts associated with the distribution of anaphors, such as long-distance binding effects and the subject-orientation of monomorphemic anaphors. Further, traditional binding theory is incompatible with minimalist assumptions. In this dissertation I propose an analysis of…

  14. Understanding Energy

    Science.gov (United States)

    Menon, Deepika; Shelby, Blake; Mattingly, Christine

    2016-01-01

    "Energy" is a term often used in everyday language. Even young children associate energy with the food they eat, feeling tired after playing soccer, or when asked to turn the lights off to save light energy. However, they may not have the scientific conceptual understanding of energy at this age. Teaching energy and matter could be…

  15. Solar Energy.

    Science.gov (United States)

    Eaton, William W.

    Presented is the utilization of solar radiation as an energy resource principally for the production of electricity. Included are discussions of solar thermal conversion, photovoltic conversion, wind energy, and energy from ocean temperature differences. Future solar energy plans, the role of solar energy in plant and fossil fuel production, and…

  16. Energy Demand

    NARCIS (Netherlands)

    Stehfest, E. et al.

    2014-01-01

    Key policy issues – How will energy demand evolve particularly in emerging and medium- and low- income economies? – What is the mix of end-use energy carriers to meet future energy demand? – How can energy efficiency contribute to reducing the growth rate of energy demand and mitigate pressures on t

  17. Glutamate Water Gates in the Ion Binding Pocket of Na+ Bound Na+, K+-ATPase

    Science.gov (United States)

    Han, Minwoo; Kopec, Wojciech; Solov’yov, Ilia A.; Khandelia, Himanshu

    2017-01-01

    The dynamically changing protonation states of the six acidic amino acid residues in the ion binding pocket of the Na+, K+ -ATPase (NKA) during the ion transport cycle are proposed to drive ion binding, release and possibly determine Na+ or K+ selectivity. We use molecular dynamics (MD) and density functional theory (DFT) simulations to determine the protonation scheme of the Na+ bound conformation of NKA. MD simulations of all possible protonation schemes show that the bound Na+ ions are most stably bound when three or four protons reside in the binding sites, and that Glu954 in site III is always protonated. Glutamic acid residues in the three binding sites act as water gates, and their deprotonation triggers water entry to the binding sites. From DFT calculations of Na+ binding energies, we conclude that three protons in the binding site are needed to effectively bind Na+ from water and four are needed to release them in the next step. Protonation of Asp926 in site III will induce Na+ release, and Glu327, Glu954 and Glu779 are all likely to be protonated in the Na+ bound occluded conformation. Our data provides key insights into the role of protons in the Na+ binding and release mechanism of NKA. PMID:28084301

  18. A computational study of ligand binding affinities in iron(III) porphine and protoporphyrin IX complexes.

    Science.gov (United States)

    Durrant, Marcus C

    2014-07-01

    The search for novel anti-malarial drugs that can disrupt biomineralization of ferriprotoporphyrin IX to haemozoin requires an understanding of the fundamental chemistry of the porphyrin's iron(iii) centre at the water-lipid interface. Towards this end, the binding affinities for a diverse set of 31 small ligands with iron(iii) porphine have been calculated using density functional theory, in the gas phase and also with implicit solvent corrections for both water and n-octanol. In addition, the binding of hydroxide, chloride, acetate, methylamine and water to ferriprotoporphyrin IX has been studied, and very similar trends are observed for the smaller and larger models. Anionic ligands generally give stronger binding than neutral ones; the strongest binding is observed for RO(-) and OH(-) ligands, whilst acetate binds relatively weakly among the anions studied. Electron-rich nitrogen donors tend to bind more strongly than electron-deficient ones, and the weakest binding is found for neutral O and S donors such as oxazole and thiophene. In all cases, ligand binding is stronger in n-octanol than in water, and the differences in binding energies for the two solvents are greater for ionic ligands than for neutrals. Finally, dimerization of ferriprotoporphyrin IX by means of iron(iii)-carboxylate bond formation has been modelled. The results are discussed in terms of haemozoin crystal growth and its disruption by known anti-malarial drugs.

  19. Ligand binding to WW tandem domains of YAP2 transcriptional regulator is under negative cooperativity.

    Science.gov (United States)

    Schuchardt, Brett J; Mikles, David C; Hoang, Lawrence M; Bhat, Vikas; McDonald, Caleb B; Sudol, Marius; Farooq, Amjad

    2014-12-01

    YES-associated protein 2 (YAP2) transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of the WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules.

  20. OB protein binds specifically to the choroid plexus of mice and rats.

    Science.gov (United States)

    Devos, R; Richards, J G; Campfield, L A; Tartaglia, L A; Guisez, Y; van der Heyden, J; Travernier, J; Plaetinck, G; Burn, P

    1996-05-28

    Binding studies were conducted to identify the anatomical location of brain target sites for OB protein, the ob gene product. 125I-labeled recombinant mouse OB protein or alkaline phosphatase-OB fusion proteins were used for in vitro and in vivo binding studies. Coronal brain sections or fresh tissue from lean, obese ob/ob, and obese db/db mice as well as lean and obese Zucker rats were probed to identify potential central OB protein-binding sites. We report here that recombinant OB protein binds specifically to the choroid plexus. The binding of OB protein (either radiolabeled or the alkaline phosphatase-OB fusion protein) and its displacement by unlabeled OB protein was similar in lean, obese ob/ob, and obese db/db mice as well as lean and obese Zucker rats. These findings suggest that OB protein binds with high affinity to a specific receptor in the choroid plexus. After binding to the choroid plexus receptor, OB protein may then be transported across the blood-brain barrier into the cerebrospinal fluid. Alternatively, binding of OB protein to a specific receptor in the choroid plexus may activate afferent neural inputs to the neural network that regulates feeding behavior and energy balance or may result in the clearance or degradation of OB protein. The identification of the choroid plexus as a brain binding site for OB protein will provide the basis for the construction of expression libraries and facilitate the rapid cloning of the choroid plexus OB receptor.

  1. Structure-based analysis of HU-DNA binding.

    Science.gov (United States)

    Swinger, Kerren K; Rice, Phoebe A

    2007-01-26

    HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently published Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from approximately 10-14.5 kcal/mol, representing K(d) values in the nanomolar to low picomolar range, and a maximum stabilization of at least approximately 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove. This is similar to sequence preferences shown by the eukaryotic nucleosome.

  2. Structure-based Analysis to Hu-DNA Binding

    Energy Technology Data Exchange (ETDEWEB)

    Swinger,K.; Rice, P.

    2007-01-01

    HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently published Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from 10-14.5 kcal/mol, representing K{sub d} values in the nanomolar to low picomolar range, and a maximum stabilization of at least 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove. This is similar to sequence preferences shown by the eukaryotic nucleosome.

  3. Synthetic heparin-binding factor analogs

    Science.gov (United States)

    Pena, Louis A.; Zamora, Paul O.; Lin, Xinhua; Glass, John D.

    2010-04-20

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  4. Defining Starch Binding by Glucan Phosphatases

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper

    2015-01-01

    phosphatases. The main objective of this study was to quantify the binding affinity of different enzymes that are involved in this cyclic process. We established a protocol to quickly, reproducibly, and quantitatively measure the binding of the enzymes to glucans utilizing Affinity Gel Electrophoresis (AGE...... glucan phosphatases showed similar affinities for the short oligosaccharide β-cyclodextrin. We performed structure-guided mutagenesis to define the mechanism of these differences. We found that the carbohydrate binding module (CBM) domain provided a stronger binding affinity compared to surface binding...

  5. Statistics for Transcription Factor Binding Sites

    OpenAIRE

    2008-01-01

    Transcription factors (TFs) play a key role in gene regulation. They interact with specific binding sites or motifs on the DNA sequence and regulate expression of genes downstream of these binding sites. In silico prediction of potential binding of a TF to a binding site is an important task in computational biology. From a statistical point of view, the DNA sequence is a long text consisting of four different letters ('A','C','G', and 'T'). The binding of a TF to the sequence corresponds to ...

  6. Interpretation of Ocular Melanin Drug Binding Assays. Alternatives to the Model of Multiple Classes of Independent Sites.

    Science.gov (United States)

    Manzanares, José A; Rimpelä, Anna-Kaisa; Urtti, Arto

    2016-04-04

    Melanin has a high binding affinity for a wide range of drugs. The determination of the melanin binding capacity and its binding affinity are important, e.g., in the determination of the ocular drug distribution, the prediction of drug effects in the eye, and the trans-scleral drug delivery. The binding parameters estimated from a given data set vary significantly when using different isotherms or different nonlinear fitting methods. In this work, the commonly used bi-Langmuir isotherm, which assumes two classes of independent sites, is confronted with the Sips isotherm. Direct, log-log, and Scatchard plots are used, and the interpretation of the binding curves in the latter is critically analyzed. In addition to the goodness of fit, the emphasis is placed on the physical meaning of the binding parameters. The bi-Langmuir model imposes a bimodal distribution of binding energies for the sites on the melanin granules, but the actual distribution is most likely continuous and unimodal, as assumed by the Sips isotherm. Hence, the latter describes more accurately the distribution of binding energies and also the experimental results of melanin binding to drugs and metal ions. Simulations are used to show that the existence of two classes of sites cannot be confirmed on the sole basis of the shape of the binding curve in the Scatchard plot, and that serious doubts may appear on the meaning of the binding parameters of the bi-Langmuir model. Experimental results of melanin binding to chloroquine and metoprolol are used to illustrate the importance of the choice of the binding isotherm and of the method used to evaluate the binding parameters.

  7. Specificity in transition state binding: the Pauling model revisited.

    Science.gov (United States)

    Amyes, Tina L; Richard, John P

    2013-03-26

    Linus Pauling proposed that the large rate accelerations for enzymes are caused by the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogues of the transition states for enzymatic reactions often act as tight-binding inhibitors provided early support for this simple and elegant proposal. We review experimental results that support the proposal that Pauling's model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high-energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies that aimed to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-coenzyme A:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of coenzyme A (CoA) are responsible for a rate increase of 3 × 10(12)-fold, which is close to the estimated total 5 × 10(13)-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide an ~12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5'-monophosphate decarboxylase, and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6-8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme

  8. Investigation of ketoprofen binding to human serum albumin by spectral methods

    Science.gov (United States)

    Bi, Shuyun; Yan, Lili; Sun, Yantao; Zhang, Hanqi

    2011-01-01

    The binding of ketoprofen with human serum albumin (HSA) was studied by fluorescence and absorption spectroscopic methods. Quenching of fluorescence of HSA was found to be a static quenching process. At 288.15, 298.15, 308.15 and 318.15 K, the binding constants and binding sites were obtained. The effects of Cu 2+, Al 3+, Ca 2+, Pb 2+ and K + on the binding at 288.15 K were also studied. The thermodynamic parameters, Δ H, Δ G and Δ S were got and the main sort of acting force between ketoprofen and HSA was studied. Based on the Förster's theory of non-radiation energy transfer, the binding average distance, r, between the acceptor (ketoprofen) and the donor (HSA) was calculated.

  9. Nanomechanical mapping of first binding steps of a virus to animal cells

    Science.gov (United States)

    Alsteens, David; Newton, Richard; Schubert, Rajib; Martinez-Martin, David; Delguste, Martin; Roska, Botond; Müller, Daniel J.

    2016-10-01

    Viral infection is initiated when a virus binds to cell surface receptors. Because the cell membrane is dynamic and heterogeneous, imaging living cells and simultaneously quantifying the first viral binding events is difficult. Here, we show an atomic force and confocal microscopy set-up that allows the surface receptor landscape of cells to be imaged and the virus binding events within the first millisecond of contact with the cell to be mapped at high resolution (virus and cell surface receptors. We find that the first bond formed between the viral glycoprotein and its cognate cell surface receptor has relatively low lifetime and free energy, but this increases as additional bonds form rapidly (≤1 ms). The formation of additional bonds occurs with positive allosteric modulation and the three binding sites of the viral glycoprotein are quickly occupied. Our quantitative approach can be readily applied to study the binding of other viruses to animal cells.

  10. Spectrophotometric analysis of flavonoid-DNA binding interactions at physiological conditions

    Science.gov (United States)

    Janjua, Naveed Kausar; Siddiqa, Asima; Yaqub, Azra; Sabahat, Sana; Qureshi, Rumana; Haque, Sayed ul

    2009-12-01

    Mode of interactions of three flavonoids [morin (M), quercetin (Q), and rutin (R)] with chicken blood ds.DNA (ck.DNA) has been investigated spectrophotometrically at different temperatures including body temperature (310 K) and at two physiological pH values, i.e. 7.4 (human blood pH) and 4.7 (stomach pH). The binding constants, Kf, evaluated using Benesi-Hildebrand equation showed that the flavonoids bind effectively through intercalation at both pH values and body temperature. Quercetin, somehow, showed greater binding capabilities with DNA. The free energies of flavonoid-DNA complexes indicated the spontaneity of their binding. The order of binding constants of three flavonoids at both pH values were found to be Kf(Q) > Kf(R) > Kf(M) and at 310 K.

  11. DBD2BS: connecting a DNA-binding protein with its binding sites

    OpenAIRE

    2012-01-01

    By binding to short and highly conserved DNA sequences in genomes, DNA-binding proteins initiate, enhance or repress biological processes. Accurately identifying such binding sites, often represented by position weight matrices (PWMs), is an important step in understanding the control mechanisms of cells. When given coordinates of a DNA-binding domain (DBD) bound with DNA, a potential function can be used to estimate the change of binding affinity after base substitutions, where the changes c...

  12. Binding equilibrium study between Mn( Ⅱ ) and HSA or BSA

    Institute of Scientific and Technical Information of China (English)

    LIANG, Hong; TU, Chu-Qiao; ZHANG, Hong-Zhi; SHEN, Xing-Can; ZHOU, Yong-Qia; SHEN, Pan-Wen

    2000-01-01

    The binding of Mn( Ⅱ ) to human serum allbumin (HSA) or bovine serum albumin (BSA) has been studied by equilibrium dialysis at physiological pH (7.43). The Scatchard analysis indicates that there are 1.8 and 1.9 strong binding sites of Mn( Ⅱ ) in HSA and BSA, respectively. The successive stobility constants which are reported for the first time are obtained by non-linear least-squares methods fitting Bjerrum formula.For both Mn( Ⅱ )-HSA and Mn( Ⅱ )-BSA systems, the order of magnitude of K1 was found to be 104. The analyses of Hill plots and free energy coupling show that the positive cooperative effect was found in both Mn( Ⅱ )-HSA and Mn(Ⅱ)-BSA systems. The results of Mn ( Ⅱ ) competing with Cu ( Ⅱ )、Zn( Ⅱ )、Cd( Ⅱ ) or Ca( Ⅱ ) to bind to HSA or BSA further support the conjecture that there are two strong binding sites of Mn( Ⅱ ) in both HSA and BSA. One is most probably located at the tripeptide segment of N-terminal sequence of HSA and BSA molecules involving four groups composed of nitrogen atoms, and the fifth coordination atom is the carboxyl oxygen of Asp1. The coordinated atoms of the other are most probably almost all oxygen atoms.

  13. Binding of fullerenes to amyloid beta fibrils: size matters.

    Science.gov (United States)

    Huy, Pham Dinh Quoc; Li, Mai Suan

    2014-10-01

    Binding affinity of fullerenes C20, C36, C60, C70 and C84 for amyloid beta fibrils is studied by docking and all-atom molecular dynamics simulations with the Amber force field and water model TIP3P. Using the molecular mechanic-Poisson Boltzmann surface area method one can demonstrate that the binding free energy linearly decreases with the number of carbon atoms of fullerene, i.e. the larger is the fullerene size, the higher is the binding affinity. Overall, fullerenes bind to Aβ9-40 fibrils stronger than to Aβ17-42. The number of water molecules trapped in the interior of 12Aβ9-40 fibrils was found to be lower than inside pentamer 5Aβ17-42. C60 destroys Aβ17-42 fibril structure to a greater extent compared to other fullerenes. Our study revealed that the van der Waals interaction dominates over the electrostatic interaction and non-polar residues of amyloid beta peptides play the significant role in interaction with fullerenes providing novel insight into the development of drug candidates against Alzheimer's disease.

  14. Infinite sets and double binds.

    Science.gov (United States)

    Arden, M

    1984-01-01

    There have been many attempts to bring psychoanalytical theory up to date. This paper approaches the problem by discussing the work of Gregory Bateson and Ignacio Matte-Blanco, with particular reference to the use made by these authors of Russell's theory of logical types. Bateson's theory of the double bind and Matte-Blanco's bilogic are both based on concepts of logical typing. It is argued that the two theories can be linked by the idea that neurotic symptoms are based on category errors in thinking. Clinical material is presented from the analysis of a middle-aged woman. The intention is to demonstrate that the process of making interpretations can be thought of as revealing errors in thinking. Changes in the patient's inner world are then seen to be the result of clarifying childhood experiences based on category errors. Matte-Blanco's theory of bilogic and infinite experiences is a re-evaluation of the place of the primary process in mental life. It is suggested that a combination of bilogic and double bind theory provides a possibility of reformulating psychoanalytical theory.

  15. Relationship between orbital energy gaps and excitation energies for long-chain systems.

    Science.gov (United States)

    Tsuneda, Takao; Singh, Raman K; Nakata, Ayako

    2016-06-15

    The difference between the excitation energies and corresponding orbital energy gaps, the exciton binding energy, is investigated based on time-dependent (TD) density functional theory (DFT) for long-chain systems: all-trans polyacetylenes and linear oligoacenes. The optimized geometries of these systems indicate that bond length alternations significantly depend on long-range exchange interactions. In TDDFT formalism, the exciton binding energy comes from the two-electron interactions between occupied and unoccupied orbitals through the Coulomb-exchange-correlation integral kernels. TDDFT calculations show that the exciton binding energy is significant when long-range exchange interactions are involved. Spin-flip (SF) TDDFT calculations are then carried out to clarify double-excitation effects in these excitation energies. The calculated SF-TDDFT results indicate that double-excitation effects significantly contribute to the excitations of long-chain systems. The discrepancies between the vertical ionization potential minus electron affinity (IP-EA) values and the HOMO-LUMO excitation energies are also evaluated for the infinitely long polyacetylene and oligoacene using the least-square fits to estimate the exciton binding energy of infinitely long systems. It is found that long-range exchange interactions are required to give the exciton binding energy of the infinitely long systems. Consequently, it is concluded that long-range exchange interactions neglected in many DFT calculations play a crucial role in the exciton binding energies of long-chain systems, while double-excitation correlation effects are also significant to hold the energy balance of the excitations. © 2016 Wiley Periodicals, Inc.

  16. UO₂²⁺ uptake by proteins: understanding the binding features of the super uranyl binding protein and design of a protein with higher affinity.

    Science.gov (United States)

    Odoh, Samuel O; Bondarevsky, Gary D; Karpus, Jason; Cui, Qiang; He, Chuan; Spezia, Riccardo; Gagliardi, Laura

    2014-12-17

    The capture of uranyl, UO2(2+), by a recently engineered protein (Zhou et al. Nat. Chem. 2014, 6, 236) with high selectivity and femtomolar sensitivity has been examined by a combination of density functional theory, molecular dynamics, and free-energy simulations. It was found that UO2(2+) is coordinated to five carboxylate oxygen atoms from four amino acid residues of the super uranyl binding protein (SUP). A network of hydrogen bonds between the amino acid residues coordinated to UO2(2+) and residues in its second coordination sphere also affects the protein's uranyl binding affinity. Free-energy simulations show how UO2(2+) capture is governed by the nature of the amino acid residues in the binding site, the integrity and strength of the second-sphere hydrogen bond network, and the number of water molecules in the first coordination sphere. Alteration of any of these three factors through mutations generally results in a reduction of the binding free energy of UO2(2+) to the aqueous protein as well as of the difference between the binding free energies of UO2(2+) and other ions (Ca(2+), Cu(2+), Mg(2+), and Zn(2+)), a proxy for the protein's selectivity over these ions. The results of our free-energy simulations confirmed the previously reported experimental results and allowed us to discover a mutant of SUP, specifically the GLU64ASP mutant, that not only binds UO2(2+) more strongly than SUP but that is also more selective for UO2(2+) over other ions. The predictions from the computations were confirmed experimentally.

  17. Configuration interaction calculations of positron binding to Be({sup 3}P )

    Energy Technology Data Exchange (ETDEWEB)

    Bromley, M.W.J. [Department of Physics, San Diego State University, San Diego, CA 92182 (United States)]. E-mail: mbromley@physics.sdsu.edu; Mitroy, J. [Faculty of Technology, Charles Darwin University, Darwin, NT 0909 (Australia)]. E-mail: jxm107@rsphysse.anu.edu.au

    2006-06-15

    The configuration interaction method is applied to investigate the possibility of positron binding to the metastable beryllium (1s{sup 2}2s2p {sup 3}P ) state. The largest calculation obtained an estimated energy that was unstable by 0.00014 Hartree with respect to the Ps + Be{sup +}(2s) lowest dissociation channel. It is likely that positron binding to parent states with non-zero angular momentum is inhibited by centrifugal barriers.

  18. Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

    Science.gov (United States)

    Moraca, Federica; Amato, Jussara; Ortuso, Francesco; Artese, Anna; Novellino, Ettore; Alcaro, Stefano; Parrinello, Michele; Limongelli, Vittorio

    2017-01-01

    G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell cycle, finally leading to apoptosis. The ability to control this mitotic clock, particularly in cancer cells, is fascinating and passes through a rational understanding of the ligand/G4 interaction. We demonstrate that an accurate description of the ligand/G4 binding mechanism is possible using an innovative free-energy method called funnel-metadynamics (FM), which we have recently developed to investigate ligand/protein interaction. Using FM simulations, we have elucidated the binding mechanism of the anticancer alkaloid berberine to the human telomeric G4 (d[AG3(T2AG3)3]), computing also the binding free-energy landscape. Two ligand binding modes have been identified as the lowest energy states. Furthermore, we have found prebinding sites, which are preparatory to reach the final binding mode. In our simulations, the ions and the water molecules have been explicitly represented and the energetic contribution of the solvent during ligand binding evaluated. Our theoretical results provide an accurate estimate of the absolute ligand/DNA binding free energy (ΔGb0 = −10.3 ± 0.5 kcal/mol) that we validated through steady-state fluorescence binding assays. The good agreement between the theoretical and experimental value demonstrates that FM is a most powerful method to investigate ligand/DNA interaction and can be a useful tool for the rational design also of G4 ligands. PMID:28232513

  19. Competition of symmetry energy and Wigner energy in nuclei

    CERN Document Server

    Tian, Junlong; Gao, Teng; Wang, Ning

    2015-01-01

    We propose a method to extract the symmetry energy coefficient (including the coefficient $a_{\\rm sym}^{(4)}$ of $I^{4}$ term) from the differences of available experimental binding energies of isobaric nuclei. The advantage of this approach is that one can efficiently remove the volume, surface and pairing energies in the process. It is found that the extracted symmetry energy coefficient $a^{*}_{\\rm sym}(A,I)$ decreases with increasing of isospin asymmetry $I$, which is mainly caused by Wigner correction, since $e^{*}_{\\rm sym}$ is the summation of the traditional symmetry energy $e_{\\rm sym}$ and the Wigner energy $e_{\\rm W}$. We obtain the optimal values $J=30.25$ MeV, $a_{\\rm ss}=56.18$ MeV, $a_{\\rm sym}^{(4)}=8.33$ MeV and the Wigner parameter $x=2.38$ through the polynomial fit to 2240 measured binding energies for nuclei with $20 \\leq A \\leq 261$ with an rms deviation of 23.42 keV. We also find that the volume-symmetry coefficient $J\\simeq 30$ MeV is insensitive to the value $x$, whereas the surface-s...

  20. Energy Management.

    Science.gov (United States)

    Bete, Tim, Ed.

    1998-01-01

    Presents the opinions of three energy experts on the issue of school facility energy management. The experts respond to the following questions: will energy deregulation occur in all 50 states and will it provide real savings; and will the majority of districts hire ESCOs to manage their energy needs? (GR)

  1. Energy Theater

    Science.gov (United States)

    Daane, Abigail R.; Wells, Lindsay; Scherr, Rachel E.

    2014-01-01

    Energy Theater is a dynamic, full-body activity that engages all students in representing the flow of energy in various phenomena, such as a light bulb burning steadily or a refrigerator cooling food. In Energy Theater, each participant acts as a unit of energy that has one form at a time. Regions on the floor correspond to objects in a physical…

  2. Hydrogen binding effect on charged P2 ( = 1-7) clusters

    Indian Academy of Sciences (India)

    Zhicong Fang; Xiangjun Kuang

    2013-11-01

    An all-electron (AE) calculation of the hydrogen binding effect on charged phosphorus clusters has been performed under the framework of density functional theory (DFT). Compared with the P$^{\\pm}_{2n}$ ( = 1-7) clusters, the HP$^{\\pm}_{2n}$ ( = 1-7), cluster has shorter average P-P bond length, larger binding energy and HOMOLUMO gap (HLG), higher chemical hardness and frequency of P-P mode. After binding with one hydrogen atom, the electronic structure is changed from open electronic shell to closed electronic shell. Geometrical stability, chemical stability and electronic stability are strengthened. These stability enhancements may be simply understood considering the electron pairing effect.

  3. The human olfactory receptor 17-40: requisites for fitting into the binding pocket.

    Science.gov (United States)

    Anselmi, Cecilia; Buonocore, Anna; Centini, Marisanna; Facino, Roberto Maffei; Hatt, Hanns

    2011-06-01

    To gain structural insight on the interactions between odorants and the human olfactory receptor, we did homology modelling of the receptor structure, followed by molecular docking simulation with ligands. Molecular dynamics simulation on the structures resulting from docking served to estimate the binding free energy of the various odorant families. A correlation with the odorous properties of the ligands is proposed. We also investigated which residues were involved in the binding of a set of properly synthesised ligands and which were required for fitting inside the binding pocket. Olfactive stimulation of the olfactory receptor with odorous molecules was also investigated, using calcium imaging or electrophysiological recordings.

  4. Fluorescence spectroscopic studies on binding of a flavonoid antioxidant quercetin to serum albumins

    Indian Academy of Sciences (India)

    Beena Mishra; Atanu Barik; K Indira Priyadarsini; Hari Mohan

    2005-11-01

    Binding of quercetin to human serum albumin (HSA) was studied and the binding constant measured by following the red-shifted absorption spectrum of quercetin in the presence of HSA and the quenching of the intrinsic protein fluorescence in the presence of different concentrations of quercetin. Fluorescence lifetime measurements of HSA showed decrease in the average lifetimes indicating binding at a location, near the tryptophan moiety, and the possibility of fluorescence energy transfer between excited tryptophan and quercetin. Critical transfer distance () was determined, from which the mean distance between tryptophan-214 in HSA and quercetin was calculated. The above studies were also carried out with bovine serum albumin (BSA).

  5. Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein

    Directory of Open Access Journals (Sweden)

    Stormo Gary D

    2005-07-01

    Full Text Available Abstract Background Recognition codes for protein-DNA interactions typically assume that the interacting positions contribute additively to the binding energy. While this is known to not be precisely true, an additive model over the DNA positions can be a good approximation, at least for some proteins. Much less information is available about whether the protein positions contribute additively to the interaction. Results Using EGR zinc finger proteins, we measure the binding affinity of six different variants of the protein to each of six different variants of the consensus binding site. Both the protein and binding site variants include single and double mutations that allow us to assess how well additive models can account for the data. For each protein and DNA alone we find that additive models are good approximations, but over the combined set of data there are context effects that limit their accuracy. However, a small modification to the purely additive model, with only three additional parameters, improves the fit significantly. Conclusion The additive model holds very well for every DNA site and every protein included in this study, but clear context dependence in the interactions was detected. A simple modification to the independent model provides a better fit to the complete data.

  6. Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein.

    Science.gov (United States)

    Li, Huameng; Li, Chenglong

    2010-07-30

    Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively.

  7. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.

    Science.gov (United States)

    Wang, Kai; Chodera, John D; Yang, Yanzhi; Shirts, Michael R

    2013-12-01

    We present a method to identify small molecule ligand binding sites and poses within a given protein crystal structure using GPU-accelerated Hamiltonian replica exchange molecular dynamics simulations. The Hamiltonians used vary from the physical end state of protein interacting with the ligand to an unphysical end state where the ligand does not interact with the protein. As replicas explore the space of Hamiltonians interpolating between these states, the ligand can rapidly escape local minima and explore potential binding sites. Geometric restraints keep the ligands from leaving the vicinity of the protein and an alchemical pathway designed to increase phase space overlap between intermediates ensures good mixing. Because of the rigorous statistical mechanical nature of the Hamiltonian exchange framework, we can also extract binding free energy estimates for all putative binding sites. We present results of this methodology applied to the T4 lysozyme L99A model system for three known ligands and one non-binder as a control, using an implicit solvent. We find that our methodology identifies known crystallographic binding sites consistently and accurately for the small number of ligands considered here and gives free energies consistent with experiment. We are also able to analyze the contribution of individual binding sites to the overall binding affinity. Our methodology points to near term potential applications in early-stage structure-guided drug discovery.

  8. Adaptive evolution of transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Berg Johannes

    2004-10-01

    Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

  9. Energy crisis

    Energy Technology Data Exchange (ETDEWEB)

    Subrahmanyam, K.V.; Mudgal, A.G. (comp.)

    1980-01-01

    Energy sources and energy consumption in India are discussed. Human and animal power constitute the principal sources of energy; both are extremely efficient users of the energy in food if they get enough; the food itself takes little energy to grow if energy-intensive agriculture does not take over from traditional methods. Of the commercial sources of energy with which India is endowed, the scarcest are natural gas and petroleum; the most abundant and reasonably well distributed geographically, except for the metallurgical grade, is coal; the one which holds out the greatest promise for the future is nuclear energy. The most important aspect of the energy problem in India is the short supply of coal to steel plants, electric utilities, and such vital industries as cement and textiles. There is a stark confession of the absence of progress on the energy front during the past 18 years. (MCW)

  10. Advantage Energy

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-07-01

    Increased focus has been placed on the issues of energy access and energy poverty over the last number of years, most notably indicated by the United Nations (UN) declaring 2012 as the 'International Year of Sustainable Energy for All'. Although attention in these topics has increased, incorrect assumptions and misunderstandings still arise in both the literature and dialogues. Access to energy does not only include electricity, does not only include cook stoves, but must include access to all types of energy that form the overall energy system. This paper chooses to examine this energy system using a typology that breaks it into 3 primary energy subsystems: heat energy, electricity and transportation. Describing the global energy system using these three subsystems provides a way to articulate the differences and similarities for each system's required investments needs by the private and public sectors.

  11. Molecular dynamics study of DNA binding by INT-DBD under a polarized force field.

    Science.gov (United States)

    Yao, Xue X; Ji, Chang G; Xie, Dai Q; Zhang, John Z H

    2013-05-15

    The DNA binding domain of transposon Tn916 integrase (INT-DBD) binds to DNA target site by positioning the face of a three-stranded antiparallel β-sheet within the major groove. As the negatively charged DNA directly interacts with the positively charged residues (such as Arg and Lys) of INT-DBD, the electrostatic interaction is expected to play an important role in the dynamical stability of the protein-DNA binding complex. In the current work, the combined use of quantum-based polarized protein-specific charge (PPC) for protein and polarized nucleic acid-specific charge (PNC) for DNA were employed in molecular dynamics simulation to study the interaction dynamics between INT-DBD and DNA. Our study shows that the protein-DNA structure is stabilized by polarization and the calculated protein-DNA binding free energy is in good agreement with the experimental data. Furthermore, our study revealed a positive correlation between the measured binding energy difference in alanine mutation and the occupancy of the corresponding residue's hydrogen bond. This correlation relation directly relates the contribution of a specific residue to protein-DNA binding energy to the strength of the hydrogen bond formed between the specific residue and DNA.

  12. Contribution of the trifluoroacetyl group in the thermodynamics of antigen-antibody binding.

    Science.gov (United States)

    Oda, Masayuki; Saito, Minoru; Tsumuraya, Takeshi; Fujii, Ikuo

    2010-01-01

    We analyzed the binding of the 7C8 antibody to the chloramphenicol phosphonate antigens-one containing a trifluoroacetyl group (CP-F) and the other containing an acetyl group (CP-H)-by using isothermal titration calorimetry (ITC). The thermodynamic difference due to the substitution of F by H was evaluated using free energy calculations based on molecular dynamics (MD) simulations. We have previously shown that another antibody, namely, 6D9, binds more weakly to CP-H than to CP-F, mainly due to the different hydration free energies of the dissociated state and not due to the unfavorable hydrophobic interactions with the antibody in the bound state. Unlike in the binding of the trifluoroacetyl group with 6D9, in its binding with 7C8, it is exposed to the solvent, as seen in the crystal structure of the complex of 7C8 with CP-F. The thermodynamic analysis performed in this study showed that the binding affinity of 7C8 for CP-H is similar to that for CP-F, but this binding to CP-H is accompanied with less favorable enthalpy and more favorable entropy changes. The free energy calculations indicated that, upon the substitution of F by H, enthalpy and entropy changes in the associated and dissociated states were decreased, but the magnitude of enthalpy and entropy changes in the dissociated state was larger than that in the associated state. The differences in binding free energy, enthalpy, and entropy changes determined by the free energy calculations for the substitution of F by H are in good agreement with the experimental results.

  13. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    Directory of Open Access Journals (Sweden)

    Selvaraj S

    2011-10-01

    Full Text Available Abstract Background Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Methods We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as binding propensity, neighboring residues in the vicinity of binding sites, conservation score and conformational switching. Results We observed that the binding propensities of amino acid residues are specific for protein-protein complexes. Further, typical dipeptides and tripeptides showed high preference for binding, which is unique to protein-protein complexes. Most of the binding site residues are highly conserved among homologous sequences. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix. Conclusions The results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.

  14. Gamma Oscillations and Visual Binding

    Science.gov (United States)

    Robinson, Peter A.; Kim, Jong Won

    2006-03-01

    At the root of visual perception is the mechanism the brain uses to analyze features in a scene and bind related ones together. Experiments show this process is linked to oscillations of brain activity in the 30-100 Hz gamma band. Oscillations at different sites have correlation functions (CFs) that often peak at zero lag, implying simultaneous firing, even when conduction delays are large. CFs are strongest between cells stimulated by related features. Gamma oscillations are studied here by modeling mm-scale patchy interconnections in the visual cortex. Resulting predictions for gamma responses to stimuli account for numerous experimental findings, including why oscillations and zero-lag synchrony are associated, observed connections with feature preferences, the shape of the zero-lag peak, and variations of CFs with attention. Gamma waves are found to obey the Schroedinger equation, opening the possibility of cortical analogs of quantum phenomena. Gamma instabilities are tied to observations of gamma activity linked to seizures and hallucinations.

  15. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

  16. DNA binding hydroxyl radical probes

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Vicky J.; Konigsfeld, Katie M.; Aguilera, Joe A. [Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610 (United States); Milligan, Jamie R., E-mail: jmilligan@ucsd.edu [Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610 (United States)

    2012-01-15

    The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores, which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA. - Highlights: > Examined four aromatic groups as a means to detect hydroxyl radicals by fluorescence. > Coumarin system suffers from the fewest disadvantages. > Characterized its reactivity when linked to a hexa-arginine peptide.

  17. Why tight-binding theory?

    Science.gov (United States)

    Harrison, Walter A.

    2002-12-01

    In the context of computational physics other methods are more accurate, but tight-binding theory allows very direct physical interpretation and is simple enough to allow much more realistic treatments beyond the local density approximation. We address several important questions of this last category: How does the gap enhancement from Coulomb correlations vary from material to material? Should the enhanced gap be used for calculating the dielectric constant? For calculating the effective mass in k-dot-p theory? How valid is the scissors approximation? How does one line up bands at an interface? How should we match the envelope function at interfaces in effective-mass theory? Why can the resulting quantum-well states seem to violate the uncertainty principle? How should f-shell electrons be treated when they are intermediate between band-like and core-like? The answers to all of these questions are given and discussed.

  18. Antiviral activity of squalamine: Role of electrostatic membrane binding

    Science.gov (United States)

    Beckerman, Bernard; Qu, Wei; Mishra, Abhijit; Zasloff, Michael; Wong, Gerard; Luijten, Erik

    2012-02-01

    Recent workootnotetextM. Zasloff et al., Proc. Nat. Acad. Sci. (USA) 108, 15978 (2011). has demonstrated that squalamine, a molecule found in the liver of sharks, exhibits broad-spectrum antiviral properties. It has been proposed that this activity results from the charge-density matching of squalamine and phospholipid membranes, causing squalamine to bind to membranes and displace proteins such as Rac1 that are crucial for the viral replication cycle. Here we investigate this hypothesis by numerical simulation of a coarse-grained model for the competition between Rac1 and squalamine in binding affinity to a flat lipid bilayer. We perform free-energy calculations to test the ability of squalamine to condense stacked bilayer systems and thereby displace bulkier Rac1 molecules. We directly compare our findings to small-angle x-ray scattering results for the same setup.

  19. Binding in light nuclei: Statistical NN uncertainties vs Computational accuracy

    Science.gov (United States)

    Navarro Pérez, R.; Nogga, A.; Amaro, J. E.; Ruiz Arriola, E.

    2016-08-01

    We analyse the impact of the statistical uncertainties of the the nucleon-nucleon interaction, based on the Granada-2013 np-pp database, on the binding energies of the triton and the alpha particle using a bootstrap method, by solving the Faddeev equations for 3H and the Yakubovsky equations for 4He respectively. We check that in practice about 30 samples prove enough for a reliable error estimate. An extrapolation of the well fulfilled Tjon-line correlation predicts the experimental binding of the alpha particle within uncertainties. Presented by RNP at Workshop for young scientists with research interests focused on physics at FAIR 14-19 February 2016 Garmisch-Partenkirchen (Germany).

  20. Exploring the ubiquinone binding cavity of respiratory complex I.

    Science.gov (United States)

    Tocilescu, Maja A; Fendel, Uta; Zwicker, Klaus; Kerscher, Stefan; Brandt, Ulrich

    2007-10-05

    Proton pumping respiratory complex I is a major player in mitochondrial energy conversion. Yet little is known about the molecular mechanism of this large membrane protein complex. Understanding the details of ubiquinone reduction will be prerequisite for elucidating this mechanism. Based on a recently published partial structure of the bacterial enzyme, we scanned the proposed ubiquinone binding cavity of complex I by site-directed mutagenesis in the strictly aerobic yeast Yarrowia lipolytica. The observed changes in catalytic activity and inhibitor sensitivity followed a consistent pattern and allowed us to define three functionally important regions near the ubiquinone-reducing iron-sulfur cluster N2. We identified a likely entry path for the substrate ubiquinone and defined a region involved in inhibitor binding within the cavity. Finally, we were able to highlight a functionally critical structural motif in the active site that consisted of Tyr-144 in the 49-kDa subunit, surrounded by three conserved hydrophobic residues.

  1. Synthetic LPS-Binding Polymer Nanoparticles

    Science.gov (United States)

    Jiang, Tian

    Lipopolysaccharide (LPS), one of the principal components of most gram-negative bacteria's outer membrane, is a type of contaminant that can be frequently found in recombinant DNA products. Because of its strong and even lethal biological effects, selective LPS removal from bioproducts solution is of particular importance in the pharmaceutical and health care industries. In this thesis, for the first time, a proof-of-concept study on preparing LPS-binding hydrogel-like NPs through facile one-step free-radical polymerization was presented. With the incorporation of various hydrophobic (TBAm), cationic (APM, GUA) monomers and cross-linkers (BIS, PEG), a small library of NPs was constructed. Their FITC-LPS binding behaviors were investigated and compared with those of commercially available LPS-binding products. Moreover, the LPS binding selectivity of the NPs was also explored by studying the NPs-BSA interactions. The results showed that all NPs obtained generally presented higher FITC-LPS binding capacity in lower ionic strength buffer than higher ionic strength. However, unlike commercial poly-lysine cellulose and polymyxin B agarose beads' nearly linear increase of FITC-LPS binding with particle concentration, NPs exhibited serious aggregation and the binding quickly saturated or even decreased at high particle concentration. Among various types of NPs, higher FITC-LPS binding capacity was observed for those containing more hydrophobic monomers (TBAm). However, surprisingly, more cationic NPs with higher content of APM exhibited decreased FITC-LPS binding in high ionic strength conditions. Additionally, when new cationic monomer and cross-linker, GUA and PEG, were applied to replace APM and BIS, the obtained NPs showed improved FITC-LPS binding capacity at low NP concentration. But compared with APM- and BIS-containing NPs, the FITC-LPS binding capacity of GUA- and PEG-containing NPs saturated earlier. To investigate the NPs' binding to proteins, we tested the NPs

  2. Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila.

    Science.gov (United States)

    Ruiz, Mario; Ganfornina, Maria D; Correnti, Colin; Strong, Roland K; Sanchez, Diego

    2014-04-01

    Lipocalins are small extracellular proteins mostly described as lipid carriers. The Drosophila lipocalin NLaz (neural Lazarillo) modulates the IIS pathway and regulates longevity, stress resistance, and behavior. Here, we test whether a native hydrophobic pocket structure is required for NLaz to perform its functions. We use a point mutation altering the binding pocket (NLaz(L130R)) and control mutations outside NLaz binding pocket. Tryptophan fluorescence titration reveals that NLaz(L130R) loses its ability to bind ergosterol and the pheromone 7(z)-tricosene but retains retinoic acid binding. Using site-directed transgenesis in Drosophila, we test the functionality of the ligand binding-altered lipocalin at the organism level. NLaz-dependent life span reduction, oxidative stress and starvation sensitivity, aging markers accumulation, and deficient courtship are rescued by overexpression of NLaz(WT), but not of NLaz(L130R). Transcriptional responses to aging and oxidative stress show a large set of age-responsive genes dependent on the integrity of NLaz binding pocket. Inhibition of IIS activity and modulation of oxidative stress and infection-responsive genes are binding pocket-dependent processes. Control of energy metabolites on starvation appears to be, however, insensitive to the modification of the NLaz binding pocket.

  3. Spectroscopic and molecular modelling studies of binding mechanism of metformin with bovine serum albumin

    Science.gov (United States)

    Sharma, Deepti; Ojha, Himanshu; Pathak, Mallika; Singh, Bhawna; Sharma, Navneet; Singh, Anju; Kakkar, Rita; Sharma, Rakesh K.

    2016-08-01

    Metformin is a biguanide class of drug used for the treatment of diabetes mellitus. It is well known that serum protein-ligand binding interaction significantly influence the biodistribution of a drug. Current study was performed to characterize the binding mechanism of metformin with serum albumin. The binding interaction of the metformin with bovine serum albumin (BSA) was examined using UV-Vis absorption spectroscopy, fluorescence, circular dichroism, density functional theory and molecular docking studies. Absorption spectra and fluorescence emission spectra pointed out the weak binding of metformin with BSA as was apparent from the slight change in absorbance and fluorescence intensity of BSA in presence of metformin. Circular dichroism study implied the significant change in the conformation of BSA upon binding with metformin. Density functional theory calculations showed that metformin has non-planar geometry and has two energy states. The docking studies evidently signified that metformin could bind significantly to the three binding sites in BSA via hydrophobic, hydrogen bonding and electrostatic interactions. The data suggested the existence of non-covalent specific binding interaction in the complexation of metformin with BSA. The present study will certainly contribute to the development of metformin as a therapeutic molecule.

  4. Thermodynamics of cationic lipid binding to DNA and DNA condensation: roles of electrostatics and hydrophobicity.

    Science.gov (United States)

    Matulis, Daumantas; Rouzina, Ioulia; Bloomfield, Victor A

    2002-06-26

    Alkylammonium binding to DNA was studied by isothermal titration calorimetry. Experimental data, obtained as functions of alkyl chain length, salt concentration, DNA concentration, and temperature, provided a detailed thermodynamic description of lipid-DNA binding reactions leading to DNA condensation. Lipid binding, counterion displacement, and DNA condensation were highly cooperative processes, driven by a large increase in entropy and opposed by a relatively small endothermic enthalpy at room temperature. Large negative heat capacity change indicated a contribution from hydrophobic interactions between aliphatic tails. An approximation of lipid-DNA binding as dominated by two factors-ionic and hydrophobic interactions-yielded a model that was consistent with experimental data. Chemical group contributions to the energetics of binding were determined and could be used to predict energetics of other lipid binding to DNA. Electrostatic and hydrophobic contributions to Gibbs free energy, enthalpy, entropy, and heat capacity could be distinguished by applying additivity principles. Binding of lipids with two, three, and four aliphatic tails was investigated and compared to single-tailed lipid binding. Structurally, the model suggests that lipid cationic headgroups and aliphatic tails distribute evenly and lay down on DNA surface without the formation of micelles.

  5. Peptide binding specificity of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Sandhu, N.; Duus, K.; Jorgensen, C.S.;

    2007-01-01

    Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length and composit......Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length...... and composition. A large set of available synthetic peptides (n=127) was tested for binding to calreticulin and the results analysed by multivariate data analysis. The parameter that correlated best with binding was hydrophobicity while beta-turn potential disfavoured binding. Only hydrophobic peptides longer...... a peptide-binding specificity for hydrophobic sequences and delineate the fine specificity of calreticulin for hydrophobic amino acid residues....

  6. The helical structure of DNA facilitates binding

    Science.gov (United States)

    Berg, Otto G.; Mahmutovic, Anel; Marklund, Emil; Elf, Johan

    2016-09-01

    The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction-diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general.

  7. Analysis of binding behavior between dynamic structures of a papain and the peptide consisting of 10 GLY residues

    Science.gov (United States)

    Nishiyama, Katsuhiko

    2010-07-01

    The binding of 10GLY to dynamic structures of papain was investigated by molecular dynamics and docking simulations. The binding free energies and sites were greatly fluctuated depending on the time and the binding was more stable and existed at the near site of active center when the structural changes in the highly flexible residues in papain were larger. Binding stability and sites would be significantly influenced by the highly flexible residues. Analysis of such residues would provide an important guideline for clarification of enzymatic activities and modification of structural dynamics of such residues would allow us to control enzymatic activities.

  8. Energy audit and energy security

    Directory of Open Access Journals (Sweden)

    Beata Agnieszka Kulessa

    2013-07-01

    Full Text Available In article, we present the issue of energy security. This article to answer the questions concerning the future of energy in Poland. These activities are directly related to energy security and the reduction of CO2 emissions. One element of this plan is the introduction in the EU energy certification of buildings. The energy certificates in Poland launched on 01.01.2009 and implements the objectives adopted by the European Union and contribute to energy security, increasing energy efficiency in construction and environmental protection.

  9. The Nuclear Symmetry Energy

    CERN Document Server

    Baldo, M

    2016-01-01

    The nuclear symmetry energy characterizes the variation of the binding energy as the neutron to proton ratio of a nuclear system is varied. This is one of the most important features of nuclear physics in general, since it is just related to the two component nature of the nuclear systems. As such it is one of the most relevant physical parameters that affect the physics of many phenomena and nuclear processes. This review paper presents a survey of the role and relevance of the nuclear symmetry energy in different fields of research and of the accuracy of its determination from the phenomenology and from the microscopic many-body theory. In recent years, a great interest was devoted not only to the Nuclear Matter symmetry energy at saturation density but also to its whole density dependence, which is an essential ingredient for our understanding of many phenomena. We analyze the nuclear symmetry energy in different realms of nuclear physics and astrophysics. In particular we consider the nuclear symmetry ene...

  10. Predicted metal binding sites for phytoremediation

    OpenAIRE

    Sharma, Ashok; Roy, Sudeep; Tripathi, Kumar Parijat; Roy, Pratibha; Mishra, Manoj; Khan, Feroz; Meena, Abha

    2009-01-01

    Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAP's). Earlier work on MAP's have shown that heavy metals accumulated by aromatic and medicinal plants do no...

  11. A computational model for feature binding

    Institute of Scientific and Technical Information of China (English)

    SHI ZhiWei; SHI ZhongZhi; LIU Xi; SHI ZhiPing

    2008-01-01

    The "Binding Problem" is an important problem across many disciplines, including psychology, neuroscience, computational modeling, and even philosophy. In this work, we proposed a novel computational model, Bayesian Linking Field Model, for feature binding in visual perception, by combining the idea of noisy neuron model, Bayesian method, Linking Field Network and competitive mechanism.Simulation Experiments demonstrated that our model perfectly fulfilled the task of feature binding in visual perception and provided us some enlightening idea for future research.

  12. A computational model for feature binding

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The "Binding Problem" is an important problem across many disciplines, including psychology, neuroscience, computational modeling, and even philosophy. In this work, we proposed a novel computational model, Bayesian Linking Field Model, for feature binding in visual perception, by combining the idea of noisy neuron model, Bayesian method, Linking Field Network and competitive mechanism. Simulation Experiments demonstrated that our model perfectly fulfilled the task of feature binding in visual perception and provided us some enlightening idea for future research.

  13. Graph Energy

    CERN Document Server

    Li, Xueliang; Gutman, Ivan

    2012-01-01

    This book is about graph energy. The authors have included many of the important results on graph energy, such as the complete solution to the conjecture on maximal energy of unicyclic graphs, the Wagner-Heuberger's result on the energy of trees, the energy of random graphs or the approach to energy using singular values. It contains an extensive coverage of recent results and a gradual development of topics and the inclusion of complete proofs from most of the important recent results in the area. The latter fact makes it a valuable reference for researchers looking to get into the field of g

  14. Lead-Binding Proteins: A Review

    Directory of Open Access Journals (Sweden)

    Harvey C. Gonick

    2011-01-01

    Full Text Available Lead-binding proteins are a series of low molecular weight proteins, analogous to metallothionein, which segregate lead in a nontoxic form in several organs (kidney, brain, lung, liver, erythrocyte. Whether the lead-binding proteins in every organ are identical or different remains to be determined. In the erythrocyte, delta-aminolevulinic acid dehydratase (ALAD isoforms have commanded the greatest attention as proteins and enzymes that are both inhibitable and inducible by lead. ALAD-2, although it binds lead to a greater degree than ALAD-1, appears to bind lead in a less toxic form. What may be of greater significance is that a low molecular weight lead-binding protein, approximately 10 kDa, appears in the erythrocyte once blood lead exceeds 39 μg/dL and eventually surpasses the lead-binding capacity of ALAD. In brain and kidney of environmentally exposed humans and animals, a cytoplasmic lead-binding protein has been identified as thymosin β4, a 5 kDa protein. In kidney, but not brain, another lead-binding protein has been identified as acyl-CoA binding protein, a 9 kDa protein. Each of these proteins, when coincubated with liver ALAD and titrated with lead, diminishes the inhibition of ALAD by lead, verifying their ability to segregate lead in a nontoxic form.

  15. Drug binding properties of neonatal albumin

    DEFF Research Database (Denmark)

    Brodersen, R; Honoré, B

    1989-01-01

    Neonatal and adult albumin was isolated by gel chromatography on Sephacryl S-300, from adult and umbilical cord serum, respectively. Binding of monoacetyl-diamino-diphenyl sulfone, warfarin, sulfamethizole, and diazepam was studied by means of equilibrium dialysis and the binding data were analyzed...... by the method of several acceptable fitted curves. It was found that the binding affinity to neonatal albumin is less than to adult albumin for monoacetyl-diamino-diphenyl sulfone and warfarin. Sulfamethizole binding to the neonatal protein is similarly reduced when more than one molecule of the drug is bound...

  16. Advances on Plant Pathogenic Mycotoxin Binding Proteins

    Institute of Scientific and Technical Information of China (English)

    WANG Chao-hua; DONG Jin-gao

    2002-01-01

    Toxin-binding protein is one of the key subjects in plant pathogenic mycotoxin research. In this paper, new advances in toxin-binding proteins of 10 kinds of plant pathogenic mycotoxins belonging to Helminthosporium ,Alternaria ,Fusicoccum ,Verticillium were reviewed, especially the techniques and methods of toxin-binding proteins of HS-toxin, HV-toxin, HMT-toxin, HC-toxin. It was proposed that the isotope-labeling technique and immunological chemistry technique should be combined together in research of toxin-binding protein, which will be significant to study the molecular recognition mechanism between host and pathogenic fungus.

  17. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  18. Binding isotope effects as a tool for distinguishing hydrophobic and hydrophilic binding sites of HIV-1 RT.

    Science.gov (United States)

    Krzemińska, Agnieszka; Paneth, Piotr; Moliner, Vicent; Świderek, Katarzyna

    2015-01-22

    The current treatment for HIV-1 infected patients consists of a cocktail of inhibitors, in an attempt to improve the potency of the drugs by adding the possible effects of each supplied compound. In this contribution, nine different inhibitors of HIV-1 RT, one of the three key proteins responsible for the virus replication, have been selected to develop and test a computational protocol that allows getting a deep insight into the inhibitors' binding mechanism. The interaction between the inhibitors and the protein have been quantified by computing binding free energies through FEP calculations, while a more detailed characterization of the kind of inhibitor-protein interactions is based on frequency analysis of the ligands in the initial and final state, i.e. in solution and binding the protein. QM/MM calculation of heavy atoms ((13)C, (15)N, and (18)O) binding isotope effects (BIE) have been used to identify the binding sites of the different inhibitors. Specific interactions between the isotopically labeled atoms of the inhibitors and polar residues and magnesium cations on the hydrophilic pocket of the protein are responsible for the frequencies shifting that can be detected when comparing the IR spectra of the compounds in solution and in the protein. On the contrary, it seems that changes in vdW interactions from solution to the final state when the ligand is interacting with residues of the hydrophobic cavity, does not influence frequency modes and then no BIE are observed. Our results suggest that a proper computational protocol can be a valuable tool which in turn can be used to increase the efficiency of anti AIDS drugs.

  19. The Q Motif Is Involved in DNA Binding but Not ATP Binding in ChlR1 Helicase.

    Directory of Open Access Journals (Sweden)

    Hao Ding

    Full Text Available Helicases are molecular motors that couple the energy of ATP hydrolysis to the unwinding of structured DNA or RNA and chromatin remodeling. The conversion of energy derived from ATP hydrolysis into unwinding and remodeling is coordinated by seven sequence motifs (I, Ia, II, III, IV, V, and VI. The Q motif, consisting of nine amino acids (GFXXPXPIQ with an invariant glutamine (Q residue, has been identified in some, but not all helicases. Compared to the seven well-recognized conserved helicase motifs, the role of the Q motif is less acknowledged. Mutations in the human ChlR1 (DDX11 gene are associated with a unique genetic disorder known as Warsaw Breakage Syndrome, which is characterized by cellular defects in genome maintenance. To examine the roles of the Q motif in ChlR1 helicase, we performed site directed mutagenesis of glutamine to alanine at residue 23 in the Q motif of ChlR1. ChlR1 recombinant protein was overexpressed and purified from HEK293T cells. ChlR1-Q23A mutant abolished the helicase activity of ChlR1 and displayed reduced DNA binding ability. The mutant showed impaired ATPase activity but normal ATP binding. A thermal shift assay revealed that ChlR1-Q23A has a melting point value similar to ChlR1-WT. Partial proteolysis mapping demonstrated that ChlR1-WT and Q23A have a similar globular structure, although some subtle conformational differences in these two proteins are evident. Finally, we found ChlR1 exists and functions as a monomer in solution, which is different from FANCJ, in which the Q motif is involved in protein dimerization. Taken together, our results suggest that the Q motif is involved in DNA binding but not ATP binding in ChlR1 helicase.

  20. Preferential binding of fisetin to the native state of bovine serum albumin: spectroscopic and docking studies.

    Science.gov (United States)

    Singha Roy, Atanu; Pandey, Nitin Kumar; Dasgupta, Swagata

    2013-04-01

    We have investigated the binding of the biologically important flavonoid fisetin with the carrier protein bovine serum albumin using multi-spectroscopic and molecular docking methods. The binding constants were found to be in the order of 10(4) M(-1) and the number of binding sites was determined as one. MALDI-TOF analyses showed that one fisetin molecule binds to a single bovine serum albumin (BSA) molecule which is also supported by fluorescence quenching studies. The negative Gibbs free energy change (∆G°) values point to a spontaneous binding process which occurs through the presence of electrostatic forces with hydrophobic association that results in a positive entropy change (+51.69 ± 1.18 J mol(-1) K(-1)). The unfolding and refolding of BSA in urea have been studied in absence and presence of fisetin using steady-state fluorescence and lifetime measurements. Urea denaturation studies indicate that fisetin is gradually released from its binding site on the protein. In the absence of urea, an increase in temperature that causes denaturation of the protein results in the release of fisetin from its bound state indicating that fisetin binds only to the native state of the protein. The circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopic studies showed an increase in % α-helix content of BSA after binding with fisetin. Site marker displacement studies in accordance with the molecular docking results suggested that fisetin binds in close proximity of the hydrophobic cavity in site 1 (subdomain IIA) of the protein. The PEARLS (Program of Energetic Analysis of Receptor Ligand System) has been used to estimate the interaction energy of fisetin with BSA and the results are in good correlation with the experimental findings.