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. Skyrmions with low binding energies

    Directory of Open Access Journals (Sweden)

    Mike Gillard

    2015-06-01

    Full Text Available Nuclear binding energies are investigated in two variants of the Skyrme model: the first replaces the usual Skyrme term with a term that is sixth order in derivatives, and the second includes a potential that is quartic in the pion fields. Solitons in the first model are shown to deviate significantly from ansätze previously assumed in the literature. The binding energies obtained in both models are lower than those obtained from the standard Skyrme model, and those obtained in the second model are close to the experimental values.

  3. Skyrmions with low binding energies

    Energy Technology Data Exchange (ETDEWEB)

    Gillard, Mike, E-mail: m.n.gillard@leeds.ac.uk; Harland, Derek, E-mail: d.g.harland@leeds.ac.uk; Speight, Martin, E-mail: speight@maths.leeds.ac.uk

    2015-06-15

    Nuclear binding energies are investigated in two variants of the Skyrme model: the first replaces the usual Skyrme term with a term that is sixth order in derivatives, and the second includes a potential that is quartic in the pion fields. Solitons in the first model are shown to deviate significantly from ansätze previously assumed in the literature. The binding energies obtained in both models are lower than those obtained from the standard Skyrme model, and those obtained in the second model are close to the experimental values.

  4. Gravitational Binding Energy in Charged Cylindrical Symmetry

    CERN Document Server

    Sharif, M

    2014-01-01

    We consider static cylindrically symmetric charged gravitating object with perfect fluid and investigate the gravitational binding energy. It is found that only the localized part of the mass function provides the gravitational binding energy, whereas the non-localized part generated by the electric coupling does not contribute for such energy.

  5. 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...

  6. 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.

  7. 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.

  8. Systematic Calculations of Total Atomic Binding Energies

    International Nuclear Information System (INIS)

    We have calculated total atomic binding energies of 3- to 91-electron ions of all atoms with Z=3 to 118, in the Dirac-Fock model, for applications to atomic mass determination from highly-charged ions. In this process we have determined the ground-state configuration of many ions for which it was not known. We also provide total electronic correlation including Breit correlation for iso-electronic series of beryllium, neon, magnesium and argon, using the multiconfiguration Dirac-Fock approach.

  9. Electron binding energies using perturbative delta-SCF method

    Science.gov (United States)

    Bhusal, Shusil; Baruah, Tunna; Zope, Rajendra

    The knowledge of fundamental and optical gaps is of significant importance for organic photovoltaics. The electron binding energies estimated from the Kohn-Sham eigenvalues are significantly underestimated. Here, we use our recently outlined perturbative delta-SCF approach to compute the electron binding energies of a number of aromatic organic molecules commonly used in organic photovoltaics. Further, the electron affinities are also computed for the C60, C70 and PCBM. The results show that the perturbative delta-SCF provide adequate description of valence electron binding energies. We also applied the method to compute the core binding energies and the core-valence excited states. While the method can successfully predict the core-valence excited states the results on the core-binding energies are mixed. The strategies for improvement of the core binding energies will be discussed.

  10. Relativistic Nuclear Energy Density Functionals: adjusting parameters to binding energies

    CERN Document Server

    Niksic, T; Ring, P

    2008-01-01

    We study a particular class of relativistic nuclear energy density functionals in which only nucleon degrees of freedom are explicitly used in the construction of effective interaction terms. Short-distance (high-momentum) correlations, as well as intermediate and long-range dynamics, are encoded in the medium (nucleon density) dependence of the strength functionals of an effective interaction Lagrangian. Guided by the density dependence of microscopic nucleon self-energies in nuclear matter, a phenomenological ansatz for the density-dependent coupling functionals is accurately determined in self-consistent mean-field calculations of binding energies of a large set of axially deformed nuclei. The relationship between the nuclear matter volume, surface and symmetry energies, and the corresponding predictions for nuclear masses is analyzed in detail. The resulting best-fit parametrization of the nuclear energy density functional is further tested in calculations of properties of spherical and deformed medium-he...

  11. Effect of Nuclear Binding Energy to K Factor

    Institute of Scientific and Technical Information of China (English)

    HOU Zhao-Yu; GUO Ai-Qiang

    2007-01-01

    We modify the square of virtual photon four-momentum by using nuclear binding energy formula,and calculate the effect of nuclear binding energy to K factor and Compton subprocess and annihilate subprocess in A-A collision Drell-Yan process.The outcome indicates that the effect of nuclear binding energy to K factor is obvious in little x region and it would disappear gradually as x increases.

  12. Experimental Binding Energies in Supramolecular Complexes.

    Science.gov (United States)

    Biedermann, Frank; Schneider, Hans-Jörg

    2016-05-11

    On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information. PMID:27136957

  13. 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...

  14. Binding-energy distribution and dephasing of localized biexcitons

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher; Umlauff, M.;

    1997-01-01

    We report on the binding energy and dephasing of localized biexciton states in narrow ZnSe multiple quantum wells. The measured binding-energy distribution of the localized biexcitons shows a width of 2.2 meV centered at 8.5 meV, and is fairly independent of the exciton localization energy. In four......-wave mixing, the biexciton photon echo decays fast and nonexponentially. This behavior results from the inhomogeneous broadening of the biexciton binding energy, as we show by a comparison with an analytical model calculation. The fast decay is thus not related to a fast microscopic biexciton dephasing....

  15. 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)

  16. Atomic Mass and Nuclear Binding Energy for Fe-52 (Iron)

    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 Fe-52 (Iron, atomic number Z = 26, mass number A = 52).

  17. Atomic Mass and Nuclear Binding Energy for Sr-71 (Strontium)

    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 Sr-71 (Strontium, atomic number Z = 38, mass number A = 71).

  18. 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....

  19. Nuclear binding energies from a BPS Skyrme model

    OpenAIRE

    Adam, C.; Naya, C.; Sanchez-Guillen, J.(Departamento de Física de Partículas, Universidad de Santiago de Compostela and Instituto Galego de Física de Altas Enerxias (IGFAE), Santiago de Compostela, E-15782, Spain); Wereszczynski, A.

    2013-01-01

    Recently, within the space of generalized Skyrme models, a BPS submodel was identified which reproduces some bulk properties of nuclear matter already on a classical level and, as such, constitutes a promising field theory candidate for the detailed and reliable description of nuclei and hadrons. Here we extend and further develop these investigations by applying the model to the calculation of nuclear binding energies. Concretely, we calculate these binding energies by including the classica...

  20. 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).

  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. The Binding Energy Parameter for Common Envelope Evolution

    CERN Document Server

    Wang, Cheng; Li, Xiang-Dong

    2016-01-01

    The binding energy parameter $\\lambda$ plays a vital role in common envelope evolution. Though it is well known that $\\lambda$ takes different values for stars with different masses and varies during stellar evolution, it has been erroneously adopted as a constant in most of the population synthesis calculations. We have systematically calculated the values of $\\lambda$ for stars of masses $1-60\\,M_{\\odot}$ by use of an updated stellar evolution code, taking into account contribution from both gravitational energy and internal energy to the binding energy of the envelope. We adopt the criterion for the core-envelope boundary advocated by \\citet{Ivanova2011}. A new kind of $\\lambda$ with the enthalpy prescription is also investigated. We present fitting formulae for the calculated values of various kinds of $\\lambda$, which can be used in future population synthesis studies.

  3. The binding energy parameter for common envelope evolution

    Science.gov (United States)

    Wang, Chen; Jia, Kun; Li, Xiang-Dong

    2016-08-01

    The binding energy parameter λ plays a vital role in common envelope evolution. Though it is well known that λ takes different values for stars with different masses and varies during stellar evolution, it has been erroneously adopted as a constant in most population synthesis calculations. We have systematically calculated the values of λ for stars of masses 1 – 60 M ⊙ by use of an updated stellar evolution code, taking into account the contribution from both gravitational energy and internal energy to the binding energy of the envelope. We adopt the criterion for the core-envelope boundary advocated by Ivanova. A new kind of λ with an enthalpy prescription is also investigated. We present fitting formulae for the calculated values of various kinds of λ, which can be used in future population synthesis studies.

  4. 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.

  5. Binding energy and stability of heavy and superheavy nuclei

    OpenAIRE

    Kolesnikov, N.N.

    2012-01-01

    Three different ways for description of binding energy of superheavy nuclei are discussed. First, one can consider superheavy nuclei as a part of a whole system of nuclei for which a global mass formula is found. Another way is the detailed local description of energy of superheavy nuclei taking into account the effects of shells and subshells. The third way of description, applied for nuclei in the region limited by principal magic numbers, is attached to the beta-stability line.

  6. 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.

  7. 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.

  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. Application of Henry's Law for Binding Energies of Adsorbed Hydrogen

    Science.gov (United States)

    Gillespie, Andrew; Dohnke, Elmar; Stalla, David; Sweany, Mark; Pfeifer, Peter

    2015-03-01

    The method of isosteres is the simplest method used to calculate the differential enthalpy of adsorption. However, it is incredibly sensitive to the choice of model and respective fitting parameters. For a set of isotherms measured on a specific sample, most models converge upon a similar value at high coverage, but are inconsistent in the low pressure regime. In this talk, we investigate the application of various models for localized and mobile adsorption at low pressures in order to obtain binding energy of hydrogen to the adsorbent surface. Henry's Law analysis of the Langmuir Model of adsorption yield binding energies in excellent agreement with those obtained from the Clausius Clapeyron relation. Work supported by DOE-EERE, Award No. DE-FG36-08GO18142.

  10. 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.

  11. 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.

  12. Pauli exclusion operator and binding energy of nuclear matter

    OpenAIRE

    Schiller, E.; Müther, H; Czerski, P.

    1998-01-01

    Brueckner-Hartree-Fock calculations are performed for nuclear matter with an exact treatment of the Pauli exclusion operator in the Bethe-Goldstone equation. The differences in the calculated binding energy, compared to the angle-average approximation, which is commonly used, are non-negligible. These difference exhibits a specific density dependence, which shifts the calculated saturation point towards smaller densities. This effect is observed for various versions of modern models for the N...

  13. Single particle spectrum and binding energy of nuclear matter

    OpenAIRE

    Baldo, M; Fiasconaro, A.

    2000-01-01

    In non-relativistic Brueckner calculations of nuclear matter, the self-consistent single particle potential is strongly momentum dependent. To simplify the calculations, a parabolic approximation is often used in the literature. The variation in the binding energy value introduced by the parabolic approximation is quantitatively analyzed in detail. It is found that the approximation can introduce an uncertainty of 1-2 MeV near the saturation density.

  14. Pauli Exclusion Operator and Binding Energy of Nuclear Matter

    International Nuclear Information System (INIS)

    Full text: Brueckner-Hartree-Fock calculations are performed for nuclear matter with an exact treatment of the Pauli exclusion operator in the Bethe-Goldstone equation. The differences in the calculated binding energy, compared to the angle-average approximation, which is commonly used, are non-negligible. These difference exhibits a specific density dependence, which shifts the calculated saturation point towards smaller densities. This effect is observed for various versions of modern models for the NN interaction. (author)

  15. 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 ...

  16. 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.

  17. 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.

  18. Binding energies of indirect excitons in double quantum well systems

    Science.gov (United States)

    Rossokhaty, Alex; Schmult, Stefan; Dietsche, Werner; von Klitzing, Klaus; Kukushkin, Igor

    2011-03-01

    A prerequisite towards Bose-Einstein condensation is a cold and dense system of bosons. Indirect excitons in double GaAs/AlGaAs quantum wells (DQWs) are believed to be suitable candidates. Indirect excitons are formed in asymmetric DQW structures by mass filtering, a method which does not require external electric fields. The exciton density and the electron-hole balance can be tuned optically. Binding energies are measured by a resonant microwave absorption technique. Our results show that screening of the indirect excitons becomes already relevant at densities as low as ~ 5 × 109 cm-2 and results in their destruction.

  19. Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.

    Science.gov (United States)

    Choi, Jeong-Mo; Serohijos, Adrian W R; Murphy, Sean; Lucarelli, Dennis; Lofranco, Leo L; Feldman, Andrew; Shakhnovich, Eugene I

    2015-02-17

    It has long been known that solvation plays an important role in protein-protein interactions. Here, we use a minimalistic solvation-based model for predicting protein binding energy to estimate quantitatively the contribution of the solvation factor in protein binding. The factor is described by a simple linear combination of buried surface areas according to amino-acid types. Even without structural optimization, our minimalistic model demonstrates a predictive power comparable to more complex methods, making the proposed approach the basis for high throughput applications. Application of the model to a proteomic database shows that receptor-substrate complexes involved in signaling have lower affinities than enzyme-inhibitor and antibody-antigen complexes, and they differ by chemical compositions on interfaces. Also, we found that protein complexes with components that come from the same genes generally have lower affinities than complexes formed by proteins from different genes, but in this case the difference originates from different interface areas. The model was implemented in the software PYTHON, and the source code can be found on the Shakhnovich group webpage: http://faculty.chemistry.harvard.edu/shakhnovich/software. PMID:25692584

  20. Charge reorganization energy and small polaron binding energy of rubrene thin films by ultraviolet photoelectron spectroscopy.

    Science.gov (United States)

    Duhm, Steffen; Xin, Qian; Hosoumi, Shunsuke; Fukagawa, Hirohiko; Sato, Kazushi; Ueno, Nobuo; Kera, Satoshi

    2012-02-14

    The hole–phonon coupling of a rubrene monolayer on graphite is measured by means of angle resolved ultraviolet photoelectron spectroscopy. Thus, the charge reorganization energy λ and the small polaron binding energy is determined, which allows insight into the nature of charge transport in condensed rubrene. PMID:22403829

  1. Decoding the nuclear genome using nuclear binding and fusion energies

    Science.gov (United States)

    Yablon, Jay R.

    2015-04-01

    In several publications the author has presented the theory that protons and neutrons and other baryons are the chromo-magnetic monopoles of Yang-Mills gauge theory and used that to deduce the up and down current quark masses from the tightly-known Q = 0 empirical electron mass and the neutron minus proton mass difference with commensurately high precision. This is then used as a springboard to closely fit a wide range of empirical nuclear binding and fusion energy data and to obtain the proton and neutron masses themselves within all experimental errors. This presentation will systematically pull all of this together and a) establishes that this way of defining current quark masses constitutes a valid measurement scheme, b) lays out the empirical support for this theory via observed nuclear binding and fusion energies as well as the proton and neutron masses themselves, c) solidifies the interface used to connect the theory to these empirical results and uncovers a mixing between the up and down current quark masses, and d) presents clearly how and why the underlying theory is very conservative, being no more and no less than a deductive mathematical synthesis of Maxwell's classical theory with both the electric and magnetic field equations merged into one, Yang-Mills gauge theory, Dirac fermion theory, the Fermi-Dirac-Pauli Exclusion Principle, and to get from classical chromodynamics to QCD, Feynman path integration.

  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. Effect of hydrostatic pressure and polaronic mass of the binding energy in a spherical quantum dot

    Institute of Scientific and Technical Information of China (English)

    A. Rejo Jeice; Sr. Gerardin Jayam; K. S. Joseph Wilson

    2015-01-01

    Simultaneous effect of hydrostatic pressure and polaronic mass on the binding energies of the ground and excited states of an on-center hydrogenic impurity confined in a GaAs/GaAlAs spherical quantum dot are theoretically investigated by the variational method within the effective mass approximation. The binding energy is calculated as a function of dot radius and pressure. Our findings proved that the hydrostatic pressure led to the decrease of confined energy and the increase of donor binding energy. Conduction band non-parabolicity and the polaron masses are effective in the donor binding energy which is significant for narrow dots not in the confined energy. The maximum donor binding energy achieved by the polaronic mass in the ground and excited states are 2%–19%for the narrow dots. The confined and donor binding energies approach zero as the dot size approaches infinity.

  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. Simultaneous effects of pressure and temperature on donor binding energy in Poeschl-Teller quantum well

    Energy Technology Data Exchange (ETDEWEB)

    Hakimyfard, Alireza; Barseghyan, M.G. [Department of Solid State Physics, Yerevan State University, Al. Manookian 1, 0025 Yerevan (Armenia); Duque, C.A., E-mail: cduque@fisica.udea.edu.c [Instituto de Fisica, Universidad de Antioquia, AA 1226, Medellin (Colombia); Kirakosyan, A.A. [Department of Solid State Physics, Yerevan State University, Al. Manookian 1, 0025 Yerevan (Armenia)

    2009-12-15

    In the frame of the variational method and the effective-mass approximation, the effects of hydrostatic pressure and temperature on the binding energy for donor impurities in the Poeschl-Teller quantum well are studied. The binding energy dependencies on the width of the quantum well, the hydrostatic pressure, the impurity position, the temperature, and the parameters of the confining potential are reported. The results show that the binding energy increases (decreases) with the increasing of the hydrostatic pressure (temperature). It is also found that, associated with the symmetry breaking in the Poeschl-Teller quantum well, and depending on the impurity position, the binding energy can increase or decrease.

  7. Transport Gap and exciton binding energy determination in organic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Krause, Stefan; Schoell, Achim; Reinert, Friedrich; Umbach, Eberhard [University of Wuerzburg (Germany). Experimental Physics II; Casu, Benedetta [Inst. f. Physik. u. Theor. Chemie, Tuebingen (Germany)

    2008-07-01

    The transport gap of an organic semiconductor is defined as the energy difference between the HOMO and LUMO levels in the presence of a hole or electron, respectively, after relaxation has occurred. Its knowledge is mandatory for the optimisation of electronic devices based on these materials. UV photoelectron spectroscopy (UPS) and inverse photoelectron spectroscopy (IPES) are routinely applied to measure these molecular levels. However, the precise determination of the transport gap on the basis of the respective data is not an easy task. It involves fundamental questions about the properties of organic molecules and their condensates, about their reaction on the experimental probe, and on the evaluation of the spectroscopic data. In particular electronic relaxation processes, which occur on the time scale of the photo excitation, have to be considered adequately. We determined the transport gap for the organic semiconductors PTCDA, Alq3, DIP, CuPc, and PBI-H4. After careful data analysis and comparison to the respective values for the optical gap we obtain values for the exciton binding energies between 0.1-0.5 eV. This is considerably smaller than commonly believed and indicates a significant delocalisation of the excitonic charge over various molecular units.

  8. 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.

  9. Total binding energy via the band structure energy of 4d group transition metals

    International Nuclear Information System (INIS)

    The binding in metals provides a basis genesis to discuss the cohesive, elastic, lattice dynamical and other allied properties of the metals. A thorough and comprehensive analysis with regard to (i) various energy terms contributing to total metallic bonding, (ii) forms of the model potential incurring the band structure part of the binding, (iii) implication of s-d hybridization and (iv) effect of electron screening, has prompted us to undertake the present study of binding in several complex metals which turn out to be superconducting at low temperatures and bear hcp, bcc and fcc configurations at room temperature i.e. yttrium (Y), zirconium (Zr), niobium (Nb), molybdenum (Mo), ruthenium (Ru), rhodium (Rh) and palladium (Pd). (author). 13 refs., 2 figs., 2 tabs

  10. 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.

  11. 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...

  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. Formation Mechanism and Binding Energy for Regular Tetrahedral Structure of Li4

    Institute of Scientific and Technical Information of China (English)

    GOU Qing-Quan; YANG Jian-Hui; LI Ping

    2006-01-01

    The formation mechanism for the regular tetrahedral structure of Li4 cluster is proposed. The curve of the total energy versus the separation R between the two nuclei has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of-29.8279 a.u. at R=14.50 a0. When R approaches infinity the total energy of four lithium atoms has the value of-29.7121 a.u. So the binding energy of Li4 with respect to four lithium atoms is the difference of 0.1158 a.u.for the above two energy values. Therefore the binding energy per atom for Li4 is 0.029 a.u., or 0.7878 eV, which is greater than the binding energy per atom of 0.453 eV for Li2, the binding energy pcr atom of 0.494 eV for Li3 and the binding energy per atom of 0.632 eV for Li5 calculated previously by us. This means that the Li4 cluster may be formed stably in a regular tetrahedral structure of side length R=14.50 a0 with a greater binding energy.

  14. Geometry, Energy, and Some Electronic Properties of Carbon Polyprismanes: Ab Initio and Tight-Binding Study

    OpenAIRE

    Konstantin P. Katin; Shostachenko, Stanislav A.; Avkhadieva, Alina I.; Mikhail M. Maslov

    2015-01-01

    We report geometry, energy, and some electronic properties of [n,4]- and [n,5]prismanes (polyprismanes): a special type of carbon nanotubes constructed from dehydrogenated cycloalkane C4- and C5-rings, respectively. Binding energies, interatomic bonds, and the energy gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) have been calculated using density functional approach and nonorthogonal tight-binding model for the systems up to thir...

  15. Implicit ligand theory: Rigorous binding free energies and thermodynamic expectations from molecular docking

    OpenAIRE

    Minh, David D. L.

    2012-01-01

    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...

  16. Formation Mechanism and Binding Energy for Body-Centred Regular Octahedral Structure of Li7 Cluster

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The formation mechanism for the body-centred regular octahedral structure of Lh cluster is proposed. The curve of the total energy versus the separation R between the nucleus at tie centre and nuclei at the apexes for this structure of Lh has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of-52.169 73 a.u. at R= 5.06a0. When R approaches infinity, the totai energy of seven lithium atoms has the value of -51.996 21 a.u. So the binding energy of Lh with respect to seven lithium atoms is 0.173 52 a.u. Therefore the binding energy per atom for hit is 0.024 79 a.u. or 0.674 eV, which is greater than the binding energy per atom of 0.453 eV for Lii, the binding energy per atom of 0.494 eV for Liz and the binding energy per atom of 0.632 eV for Li& calculated previously by us. This means that the Lh cluster may be formed stably in a body-centred regular octahedral structure with a greater binding energy.

  17. 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.

  18. 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

    Gibbs free binding energies in molecular complexes and clusters based on gas phase FTIR spectroscopy. The acetonitrile-HCl molecular complex is identified via its redshifted H-Cl stretching vibrational mode. We determine the Gibbs free binding energy, ΔG°295 K, to between 4.8 and 7.9 kJ mol(-1) and......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 of the...

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

    Science.gov (United States)

    He, Jiao; Acharyya, Kinsuk; Vidali, Gianfranco

    2016-07-01

    We measured the binding energy of N2, CO, O2, CH4, and CO2 on non-porous (compact) amorphous solid water (np-ASW), of N2 and CO on porous ASW, and of NH3 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 CO2 forms clusters on the np-ASW surface even at very low coverages. The binding energies of N2, CO, O2, and CH4 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 binding energy in the submonolayer regime, a fraction of all these ices remains for much longer and up to higher temperatures on the grain surface compared to the single value energies currently used in the astrochemical models.

  20. Calculations of the Triton Binding Energy with a Lorentz Boosted Nucleon-Nucleon Potential

    Directory of Open Access Journals (Sweden)

    Elster Ch.

    2010-04-01

    Full Text Available We study the binding energy of the three-nucleon system in relativistic models that use two different relativistic treatments of the potential that are phase equivalent to realistic NN interactions. One is based on a unitary scale transformation that relates the non-relativistic center-of-mass Hamiltonian to the relativistic mass (rest energy operator and the other uses a non-linear equation that relates the interaction in the relativistic mass operator to the non-relativistic interaction. In both cases Lorentz-boosted interactions are used in the relativistic Faddeev equation to solve for the three-nucleon binding energy. Using the same realistic NN potentials as input, the solution of the relativistic three-nucleon Faddeev equation for 3H shows slightly less binding energy than the corresponding nonrelativistic result. The effect of the Wigner spin rotation on the binding is very small.

  1. 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.

  2. Formation Mechanism and Binding Energy for Body-Centred Regular Tetrahedral Structure of Li5

    Institute of Scientific and Technical Information of China (English)

    LI Ping; YANG Jian-Hui; GOU Qing-Quan

    2006-01-01

    The formation mechanism for the body-centred regular tetrahedral structure of Li5 cluster is proposed.The curve of the total energy versus the separation R between the nucleus at the centre and nuclei at the apexes for this structure of Li5 has been calculated by using the method of Gou's modified arrangement channel quantum mechanics(MACQM). The result shows that the curve has a minimal energy of-37.2562 a.u. at R = 14.5a0. When R approaches infinity the total energy of five lithium atoms has the value of-37.1401 a.u. So the binding energy of Li5 with respect to five lithium atoms is the difference of 0.1161 a.u. for the above two energy values. Therefore the binding energy per atom for Li5 is 0.023 22 a.u., or 0.632 eV, which is greater than the binding energy per atom of 0.453 eV for Li2 and the binding energy per atom of 0.494 eV for Li3 calculated previously by us. This means that the Li5 cluster may be formed stably in a body-centred regular tetrahedral structure with a greater binding energy.

  3. 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....

  4. Effect of a high intensity laser beam on impurity binding energy in a nanocone

    Science.gov (United States)

    Paredes, H.; Beltrán Ríos, C. L.; Gutíerrez, W.

    2016-02-01

    This paper presents theoretical results of a study that analyzed the effect of a high- frequency laser in the ground state binding energy of a hydrogenic donnor impurity. For these results, the trigonometric sweep method and framework of the effective mass approximation is applied. The results showed that the binding energy changes depending on the laser intensity and the impurity position across of the nanocone axis. The results agree with previous results obtained in similar systems.

  5. Prediction of SAMPL3 Host-Guest Affinities with the Binding Energy Distribution Analysis Method (BEDAM)

    OpenAIRE

    Gallicchio, Emilio; Ronald M Levy

    2012-01-01

    BEDAM calculations are described to predict the free energies of binding of a series of anaesthetic drugs to a recently characterized acyclic cucurbituril host. The modeling predictions, conducted as part of the SAMPL3 host-guest affinity blind challenge, are generally in good quantitative agreement with the experimental measurements. The correlation coefficient between computed and measured binding free energies is 70% with high statistical significance. Multiple conformational stereoisomers...

  6. Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model

    OpenAIRE

    Muddana, Hari S.; Gilson, Michael K.

    2012-01-01

    The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy functi...

  7. Ion Binding Energies Determining Functional Transport of ClC Proteins

    Science.gov (United States)

    Yu, Tao; Guo, Xu; Zou, Xian-Wu; Sang, Jian-Ping

    2014-06-01

    The ClC-type proteins, a large family of chloride transport proteins ubiquitously expressed in biological organisms, have been extensively studied for decades. Biological function of ClC proteins can be reflected by analyzing the binding situation of Cl- ions. We investigate ion binding properties of ClC-ec1 protein with the atomic molecular dynamics simulation approach. The calculated electrostatic binding energy results indicate that Cl- at the central binding site Scen has more binding stability than the internal binding site Sint. Quantitative comparison between the latest experimental heat release data isothermal titration calorimetry (ITC) and our calculated results demonstrates that chloride ions prefer to bind at Scen than Sint in the wild-type ClC-ec1 structure and prefer to bind at Sext and Scen than Sint in mutant E148A/E148Q structures. Even though the chloride ions make less contribution to heat release when binding to Sint and are relatively unstable in the Cl- pathway, they are still part contributors for the Cl- functional transport. This work provides a guide rule to estimate the importance of Cl- at the binding sites and how chloride ions have influences on the function of ClC proteins.

  8. Quantum Monte Carlo calculation of the binding energy of the beryllium dimer

    Energy Technology Data Exchange (ETDEWEB)

    Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D. [Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 (United States)

    2015-08-28

    The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be{sub 2} is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be{sub 2} from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be{sub 2}, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm{sup −1}, only slightly below the 935 cm{sup −1} value derived from experiment.

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

    Directory of Open Access Journals (Sweden)

    Marharyta Petukh

    2016-04-01

    Full Text Available 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/.

  10. Formation Mechanism and Binding Energy for Regular Octahedral Structure of Li6 Cluster

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yan-Ping; LI Ping; GOU Qing-Quan; LIU Wei-Na

    2008-01-01

    The formation mechanism for the regular octahedral structure of Li6cluster is proposed. The curve of the total energy versus the separation R between any two neighboring nuclei has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of-44.736 89 a.u. At R=5.07α0. When R approaches infinity, the total energy of six lithium atoms has the value of-44.568 17 a.u. So the binding energy of Li6 with respect to six lithium atoms is 0.1687 a.u. Therefore, the binding energy per atom for Li6 is 0.028 12 a.u., or 0.7637 eV, which is greater than the binding energy per atom of 0.453 eV for Li2 arid the binding energy per atom of 0.494 eV for Li3 calculated in our previous work. This means that the Li6 cluster may be formed in a regular octahedral structure with a greater binding energy.

  11. 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.

  12. Formation Mechanism and Binding Energy for Equilateral Triangle Structure of Li3 Cluster

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The formation mechanism for the equilateral triangle structure of Li3 cluster is proposed. The curve of the total energy versus the interatomic distance for this structure has been calculated by using the method of Gou's Modified Arrangement Channel Quantum Mechanics. The result shows that the curve has a minimal energy of-22.338 60 a.u at R = 5.82 a0. The total energy of Li3 when R approaches ∞ has the value of-22.284 09 a.u. This is also the total energy of three lithium atoms dissociated from Li3. The difference value of 0.0545 08 a.u. for the above two energy values is the dissociation energy of Li3 cluster, which is also its binding energy. Therefore the binding energy per lithium atom for Li3 is 0.018 169 a.u. = 0.494 eV, which is greater than the binding energy of 0.453 eV per atom for Li2 calculated in a previous work. This means that the Li3 cluster may be formed in the equilateral triangle structure of side length R = 5.82a0 stably with a stronger binding from the symmetrical interaction among the three lithium atoms.

  13. 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.

  14. 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...

  15. Theoretical prediction of the binding free energy for mutants of replication protein A.

    Science.gov (United States)

    Carra, Claudio; Saha, Janapriya; Cucinotta, Francis A

    2012-07-01

    The replication protein A (RPA) is a heterotrimeric (70, 32, and 14 kDa subunits), single stranded DNA (ssDNA) binding protein required for pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Studies based on deletions and mutations have identified the high affinity ssDNA binding domains in the 70 kDa subunit of RPA, regions A and B. Individually, the domain A and B have a low affinity for ssDNA, while tandems composed of AA, AB, BB, and BA sequences bind the ssDNA with moderate to high affinity. Single and double point mutations on polar residues in the binding domains leads to a reduction in affinity of RPA for ssDNA, in particular when two hydrophilic residues are involved. In view of these results, we performed a study based on molecular dynamics simulation aimed to reproduce the experimental change in binding free energy, ΔΔG, of RPA70 mutants to further elucidate the nature of the protein-ssDNA interaction. The MM-PB(GB)SA methods implemented in Amber10 and the code FoldX were used to estimate the binding free energy. The theoretical and experimental ΔΔG values correlate better when the results are obtained by MM-PBSA calculated on individual trajectories for each mutant. In these conditions, the correlation coefficient between experimental and theoretical ΔΔG reaches a value of 0.95 despite the overestimation of the energy change by one order of magnitude. The decomposition of the MM-GBSA energy per residue allows us to correlate the change of the affinity with the residue polarity and energy contribution to the binding. The method revealed reliable predictions of the change in the affinity in function of mutations, and can be used to identify new mutants with distinct binding properties. PMID:22160652

  16. Atomic Mass and NuclearBinding Energy for Uup-269(Ununpentium)

    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 Uup-269 (Ununpentium, atomic number Z = 115, mass number A = 269).

  17. Atomic Mass and NuclearBinding Energy for Uup-335(Ununpentium)

    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 Uup-335 (Ununpentium, atomic number Z = 115, mass number A = 335).

  18. Atomic Mass and NuclearBinding Energy for Uup-332(Ununpentium)

    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 Uup-332 (Ununpentium, atomic number Z = 115, mass number A = 332).

  19. Atomic Mass and NuclearBinding Energy for Uup-326(Ununpentium)

    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 Uup-326 (Ununpentium, atomic number Z = 115, mass number A = 326).

  20. Atomic Mass and NuclearBinding Energy for Uup-259(Ununpentium)

    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 Uup-259 (Ununpentium, atomic number Z = 115, mass number A = 259).

  1. Atomic Mass and NuclearBinding Energy for Uup-300(Ununpentium)

    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 Uup-300 (Ununpentium, atomic number Z = 115, mass number A = 300).

  2. Atomic Mass and NuclearBinding Energy for Uup-317(Ununpentium)

    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 Uup-317 (Ununpentium, atomic number Z = 115, mass number A = 317).

  3. Atomic Mass and NuclearBinding Energy for Uup-304(Ununpentium)

    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 Uup-304 (Ununpentium, atomic number Z = 115, mass number A = 304).

  4. Atomic Mass and NuclearBinding Energy for Uup-276(Ununpentium)

    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 Uup-276 (Ununpentium, atomic number Z = 115, mass number A = 276).

  5. Atomic Mass and NuclearBinding Energy for Uup-271(Ununpentium)

    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 Uup-271 (Ununpentium, atomic number Z = 115, mass number A = 271).

  6. Atomic Mass and NuclearBinding Energy for Uup-321(Ununpentium)

    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 Uup-321 (Ununpentium, atomic number Z = 115, mass number A = 321).

  7. Atomic Mass and NuclearBinding Energy for Uup-294(Ununpentium)

    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 Uup-294 (Ununpentium, atomic number Z = 115, mass number A = 294).

  8. Atomic Mass and NuclearBinding Energy for Uup-277(Ununpentium)

    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 Uup-277 (Ununpentium, atomic number Z = 115, mass number A = 277).

  9. Atomic Mass and NuclearBinding Energy for Uup-310(Ununpentium)

    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 Uup-310 (Ununpentium, atomic number Z = 115, mass number A = 310).

  10. Atomic Mass and NuclearBinding Energy for Uup-306(Ununpentium)

    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 Uup-306 (Ununpentium, atomic number Z = 115, mass number A = 306).

  11. Atomic Mass and NuclearBinding Energy for Uup-323(Ununpentium)

    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 Uup-323 (Ununpentium, atomic number Z = 115, mass number A = 323).

  12. Atomic Mass and NuclearBinding Energy for Uup-299(Ununpentium)

    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 Uup-299 (Ununpentium, atomic number Z = 115, mass number A = 299).

  13. Atomic Mass and NuclearBinding Energy for Uup-286(Ununpentium)

    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 Uup-286 (Ununpentium, atomic number Z = 115, mass number A = 286).

  14. Atomic Mass and NuclearBinding Energy for Uup-282(Ununpentium)

    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 Uup-282 (Ununpentium, atomic number Z = 115, mass number A = 282).

  15. Atomic Mass and NuclearBinding Energy for Uup-338(Ununpentium)

    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 Uup-338 (Ununpentium, atomic number Z = 115, mass number A = 338).

  16. Atomic Mass and NuclearBinding Energy for Uup-324(Ununpentium)

    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 Uup-324 (Ununpentium, atomic number Z = 115, mass number A = 324).

  17. Atomic Mass and NuclearBinding Energy for Uup-322(Ununpentium)

    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 Uup-322 (Ununpentium, atomic number Z = 115, mass number A = 322).

  18. Atomic Mass and NuclearBinding Energy for Uup-305(Ununpentium)

    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 Uup-305 (Ununpentium, atomic number Z = 115, mass number A = 305).

  19. Atomic Mass and NuclearBinding Energy for Uup-336(Ununpentium)

    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 Uup-336 (Ununpentium, atomic number Z = 115, mass number A = 336).

  20. Atomic Mass and NuclearBinding Energy for Uup-308(Ununpentium)

    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 Uup-308 (Ununpentium, atomic number Z = 115, mass number A = 308).

  1. Atomic Mass and NuclearBinding Energy for Uup-291(Ununpentium)

    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 Uup-291 (Ununpentium, atomic number Z = 115, mass number A = 291).

  2. Atomic Mass and NuclearBinding Energy for Uup-320(Ununpentium)

    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 Uup-320 (Ununpentium, atomic number Z = 115, mass number A = 320).

  3. Atomic Mass and NuclearBinding Energy for Uup-261(Ununpentium)

    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 Uup-261 (Ununpentium, atomic number Z = 115, mass number A = 261).

  4. Atomic Mass and NuclearBinding Energy for Uup-296(Ununpentium)

    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 Uup-296 (Ununpentium, atomic number Z = 115, mass number A = 296).

  5. Atomic Mass and NuclearBinding Energy for Uup-272(Ununpentium)

    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 Uup-272 (Ununpentium, atomic number Z = 115, mass number A = 272).

  6. Atomic Mass and NuclearBinding Energy for Uup-258(Ununpentium)

    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 Uup-258 (Ununpentium, atomic number Z = 115, mass number A = 258).

  7. Atomic Mass and NuclearBinding Energy for Uup-273(Ununpentium)

    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 Uup-273 (Ununpentium, atomic number Z = 115, mass number A = 273).

  8. Atomic Mass and NuclearBinding Energy for Uup-302(Ununpentium)

    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 Uup-302 (Ununpentium, atomic number Z = 115, mass number A = 302).

  9. Atomic Mass and NuclearBinding Energy for Uup-289(Ununpentium)

    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 Uup-289 (Ununpentium, atomic number Z = 115, mass number A = 289).

  10. Atomic Mass and NuclearBinding Energy for Uup-334(Ununpentium)

    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 Uup-334 (Ununpentium, atomic number Z = 115, mass number A = 334).

  11. Atomic Mass and NuclearBinding Energy for Uup-316(Ununpentium)

    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 Uup-316 (Ununpentium, atomic number Z = 115, mass number A = 316).

  12. Atomic Mass and NuclearBinding Energy for Uup-309(Ununpentium)

    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 Uup-309 (Ununpentium, atomic number Z = 115, mass number A = 309).

  13. Atomic Mass and NuclearBinding Energy for Uup-262(Ununpentium)

    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 Uup-262 (Ununpentium, atomic number Z = 115, mass number A = 262).

  14. Atomic Mass and NuclearBinding Energy for Uup-319(Ununpentium)

    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 Uup-319 (Ununpentium, atomic number Z = 115, mass number A = 319).

  15. Atomic Mass and NuclearBinding Energy for Uup-314(Ununpentium)

    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 Uup-314 (Ununpentium, atomic number Z = 115, mass number A = 314).

  16. Atomic Mass and NuclearBinding Energy for Uup-281(Ununpentium)

    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 Uup-281 (Ununpentium, atomic number Z = 115, mass number A = 281).

  17. Atomic Mass and NuclearBinding Energy for Uup-267(Ununpentium)

    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 Uup-267 (Ununpentium, atomic number Z = 115, mass number A = 267).

  18. Atomic Mass and NuclearBinding Energy for Uup-329(Ununpentium)

    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 Uup-329 (Ununpentium, atomic number Z = 115, mass number A = 329).

  19. Atomic Mass and NuclearBinding Energy for Uup-264(Ununpentium)

    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 Uup-264 (Ununpentium, atomic number Z = 115, mass number A = 264).

  20. Atomic Mass and NuclearBinding Energy for Uup-298(Ununpentium)

    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 Uup-298 (Ununpentium, atomic number Z = 115, mass number A = 298).

  1. Atomic Mass and NuclearBinding Energy for Uup-339(Ununpentium)

    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 Uup-339 (Ununpentium, atomic number Z = 115, mass number A = 339).

  2. Atomic Mass and NuclearBinding Energy for Uup-278(Ununpentium)

    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 Uup-278 (Ununpentium, atomic number Z = 115, mass number A = 278).

  3. Atomic Mass and NuclearBinding Energy for Uup-312(Ununpentium)

    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 Uup-312 (Ununpentium, atomic number Z = 115, mass number A = 312).

  4. Atomic Mass and NuclearBinding Energy for Uup-318(Ununpentium)

    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 Uup-318 (Ununpentium, atomic number Z = 115, mass number A = 318).

  5. Atomic Mass and NuclearBinding Energy for Uup-270(Ununpentium)

    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 Uup-270 (Ununpentium, atomic number Z = 115, mass number A = 270).

  6. Atomic Mass and NuclearBinding Energy for Uup-263(Ununpentium)

    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 Uup-263 (Ununpentium, atomic number Z = 115, mass number A = 263).

  7. Atomic Mass and NuclearBinding Energy for Uup-313(Ununpentium)

    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 Uup-313 (Ununpentium, atomic number Z = 115, mass number A = 313).

  8. Atomic Mass and NuclearBinding Energy for Uup-337(Ununpentium)

    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 Uup-337 (Ununpentium, atomic number Z = 115, mass number A = 337).

  9. Atomic Mass and NuclearBinding Energy for Uup-287(Ununpentium)

    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 Uup-287 (Ununpentium, atomic number Z = 115, mass number A = 287).

  10. Atomic Mass and NuclearBinding Energy for Uup-279(Ununpentium)

    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 Uup-279 (Ununpentium, atomic number Z = 115, mass number A = 279).

  11. Atomic Mass and NuclearBinding Energy for Uup-275(Ununpentium)

    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 Uup-275 (Ununpentium, atomic number Z = 115, mass number A = 275).

  12. Atomic Mass and NuclearBinding Energy for Uup-333(Ununpentium)

    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 Uup-333 (Ununpentium, atomic number Z = 115, mass number A = 333).

  13. Atomic Mass and NuclearBinding Energy for Uup-280(Ununpentium)

    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 Uup-280 (Ununpentium, atomic number Z = 115, mass number A = 280).

  14. Atomic Mass and NuclearBinding Energy for Uup-266(Ununpentium)

    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 Uup-266 (Ununpentium, atomic number Z = 115, mass number A = 266).

  15. Atomic Mass and NuclearBinding Energy for Uup-330(Ununpentium)

    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 Uup-330 (Ununpentium, atomic number Z = 115, mass number A = 330).

  16. Atomic Mass and NuclearBinding Energy for Uup-265(Ununpentium)

    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 Uup-265 (Ununpentium, atomic number Z = 115, mass number A = 265).

  17. Atomic Mass and NuclearBinding Energy for Uup-283(Ununpentium)

    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 Uup-283 (Ununpentium, atomic number Z = 115, mass number A = 283).

  18. Atomic Mass and NuclearBinding Energy for Uup-297(Ununpentium)

    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 Uup-297 (Ununpentium, atomic number Z = 115, mass number A = 297).

  19. Atomic Mass and NuclearBinding Energy for Uup-268(Ununpentium)

    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 Uup-268 (Ununpentium, atomic number Z = 115, mass number A = 268).

  20. Atomic Mass and NuclearBinding Energy for Uup-274(Ununpentium)

    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 Uup-274 (Ununpentium, atomic number Z = 115, mass number A = 274).

  1. Atomic Mass and NuclearBinding Energy for Uup-260(Ununpentium)

    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 Uup-260 (Ununpentium, atomic number Z = 115, mass number A = 260).

  2. Atomic Mass and NuclearBinding Energy for Uup-307(Ununpentium)

    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 Uup-307 (Ununpentium, atomic number Z = 115, mass number A = 307).

  3. Atomic Mass and NuclearBinding Energy for Uup-293(Ununpentium)

    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 Uup-293 (Ununpentium, atomic number Z = 115, mass number A = 293).

  4. Atomic Mass and NuclearBinding Energy for Uup-284(Ununpentium)

    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 Uup-284 (Ununpentium, atomic number Z = 115, mass number A = 284).

  5. Atomic Mass and NuclearBinding Energy for Uup-292(Ununpentium)

    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 Uup-292 (Ununpentium, atomic number Z = 115, mass number A = 292).

  6. Atomic Mass and NuclearBinding Energy for Uup-328(Ununpentium)

    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 Uup-328 (Ununpentium, atomic number Z = 115, mass number A = 328).

  7. Atomic Mass and NuclearBinding Energy for Uup-331(Ununpentium)

    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 Uup-331 (Ununpentium, atomic number Z = 115, mass number A = 331).

  8. Atomic Mass and NuclearBinding Energy for Uup-311(Ununpentium)

    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 Uup-311 (Ununpentium, atomic number Z = 115, mass number A = 311).

  9. Atomic Mass and NuclearBinding Energy for Uup-285(Ununpentium)

    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 Uup-285 (Ununpentium, atomic number Z = 115, mass number A = 285).

  10. Atomic Mass and NuclearBinding Energy for Uup-315(Ununpentium)

    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 Uup-315 (Ununpentium, atomic number Z = 115, mass number A = 315).

  11. Atomic Mass and NuclearBinding Energy for Uup-288(Ununpentium)

    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 Uup-288 (Ununpentium, atomic number Z = 115, mass number A = 288).

  12. Atomic Mass and NuclearBinding Energy for Uup-295(Ununpentium)

    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 Uup-295 (Ununpentium, atomic number Z = 115, mass number A = 295).

  13. Atomic Mass and NuclearBinding Energy for Uup-301(Ununpentium)

    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 Uup-301 (Ununpentium, atomic number Z = 115, mass number A = 301).

  14. Atomic Mass and NuclearBinding Energy for Uup-303(Ununpentium)

    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 Uup-303 (Ununpentium, atomic number Z = 115, mass number A = 303).

  15. Atomic Mass and NuclearBinding Energy for Uup-290(Ununpentium)

    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 Uup-290 (Ununpentium, atomic number Z = 115, mass number A = 290).

  16. Atomic Mass and NuclearBinding Energy for Uup-327(Ununpentium)

    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 Uup-327 (Ununpentium, atomic number Z = 115, mass number A = 327).

  17. Atomic Mass and NuclearBinding Energy for Uup-325(Ununpentium)

    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 Uup-325 (Ununpentium, atomic number Z = 115, mass number A = 325).

  18. Nuclear binding energies: global collective structures and local shell-model correlations

    International Nuclear Information System (INIS)

    In this contribution the global behaviour of nuclear binding energies, or alternatively two-neutron separation energies, are studied. Recent high-precision mass measurements show local deviations from an overall macroscopic behaviour, and it is shown how a consistent and simultaneously description of both can be given within the Interacting Boson Model. (orig.)

  19. 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.

  20. Formation Mechanism and Binding Energy for Body-Centred Regular Icosahedral Structure of Li13 Cluster

    Institute of Scientific and Technical Information of China (English)

    LIU Wei-Na; LI Ping; GOU Qing-Quan; ZHAO Yan-Ping

    2008-01-01

    The formation mechanism for the body-centred regular icosahedral structure of Li13 cluster is proposed. The curve of the total energy versus the separation R between the nucleus at the centre and nuclei at the apexes for this structure of Li13 has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of-96.951 39 a.u. at R = 5.46a0. When R approaches to infinity, the total energy of thirteen lithium atoms has the value of-96.564 38 a.u. So the binding energy of Li13 with respect to thirteen lithium atoms is 0.387 01 a.u. Therefore the binding energy per atom for Li13 is 0.029 77 a.u. or 0.810 eV, which is greater than the binding energy per atom of 0.453 eV for Li2, 0.494 eV for Lia, 0.7878 eV for Li4, 0.632 eV for Lis, and 0.674 eV for Lit calculated by us previously. This means that the Li13 cluster may be formed stably in a body-centred regular icosahedral structure with a greater binding energy.

  1. Odd-even staggering of binding energy for nuclei in the s d shell

    Science.gov (United States)

    Fu, G. J.; Cheng, Y. Y.; Jiang, H.; Zhao, Y. M.; Arima, A.

    2016-08-01

    In this paper we study odd-even staggering phenomena of binding energy in the framework of the nuclear shell model for nuclei in the s d shell. We decompose the USDB effective interaction into the monopole interaction and multipole (residual) interactions. We extract the empirical proton-neutron interaction, the Wigner energy, and the one-neutron separation energy using calculated binding energies. The monopole interaction, which represents the spherical mean field, provides contributions to the empirical proton-neutron interaction, the symmetry energy, and the Wigner energy. It does not induce odd-even staggering of the empirical proton-neutron interaction or the one-neutron separation energy. Isovector monopole and quadrupole pairing interactions and isoscalar spin-1 pairing interactions play a key role in reproducing an additional binding energy in both even-even and odd-odd nuclei. The Wigner energy coefficients are sensitive to residual two-body interactions. The nuclear shell structure has a strong influence on the evolution of the one-neutron separation energy, but not on empirical proton-neutron interactions. The so-called three-point formula is a good probe of the shell structure.

  2. 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.

  3. 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. PMID:27517768

  4. 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.

  5. 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.

  6. Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.

    Science.gov (United States)

    Ohno, Kazuki; Mitsui, Takashi; Tanida, Yoshiaki; Matsuura, Azuma; Fujitani, Hideaki; Niimi, Tatsuya; Orita, Masaya

    2011-02-01

    Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein/ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1)/inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects. PMID:20480380

  7. SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates.

    Directory of Open Access Journals (Sweden)

    Seungpyo Hong

    Full Text Available SH3 domains mediate signal transduction by recognizing short peptides. Understanding of the driving forces in peptide recognitions will help us to predict the binding specificity of the domain-peptide recognition and to understand the molecular interaction networks of cells. However, accurate calculation of the binding energy is a tough challenge. In this study, we propose three ideas for improving our ability to predict the binding energy between SH3 domains and peptides: (1 utilizing the structural ensembles sampled from a molecular dynamics simulation trajectory, (2 utilizing multiple peptide templates, and (3 optimizing the sequence-structure mapping. We tested these three ideas on ten previously studied SH3 domains for which SPOT analysis data were available. The results indicate that calculating binding energy using the structural ensemble was most effective, clearly increasing the prediction accuracy, while the second and third ideas tended to give better binding energy predictions. We applied our method to the five SH3 targets in DREAM4 Challenge and selected the best performing method.

  8. Improved ligand binding energies derived from molecular dynamics: replicate sampling enhances the search of conformational space.

    Science.gov (United States)

    Adler, Marc; Beroza, Paul

    2013-08-26

    Does a single molecular trajectory provide an adequate sample conformational space? Our calculations indicate that for Molecular Mechanics--Poisson-Boltzmann Surface Area (MM-PBSA) measurement of protein ligand binding, a single molecular dynamics trajectory does not provide a representative sampling of phase space. For a single trajectory, the binding energy obtained by averaging over a number of molecular dynamics frames in an equilibrated system will converge after an adequate simulation time. A separate trajectory with nearly identical starting coordinates (1% randomly perturbed by 0.001 Å), however, can lead to a significantly different calculated binding energy. Thus, even though the calculated energy converges for a single molecular dynamics run, the variation across separate runs implies that a single run inadequately samples the system. The divergence in the trajectories is reflected in the individual energy components, such as the van der Waals and the electrostatics terms. These results indicate that the trajectories sample different conformations that are not in rapid exchange. Extending the length of the dynamics simulation does not resolve the energy differences observed between different trajectories. By averaging over multiple simulations, each with a nearly equivalent starting structure, we find the standard deviation in the calculated binding energy to be ∼1.3 kcal/mol. The work presented here indicates that combining MM-PBSA with multiple samples of the initial starting coordinates will produce more precise and accurate estimates of protein/ligand affinity. PMID:23845109

  9. 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.

  10. 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.

  11. 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.

  12. Binding energy of a bound polaron in a quantum well wire

    International Nuclear Information System (INIS)

    Theoretical study of the binding energies of an off-center donor hydrogenic impurity in a cylindrical quantum well wires semiconductor is presented. Calculations are performed in the framework of the effective mass approximation using the variational approach. We describe the effect of the quantum confinement by an infinitely deep potential well and we take into consideration the interaction between the charge carrier (electron and ion) and the optical phonons (confined longitudinal optical and surface optical). Our results show that the impunity binding energy depends strongly on the spatial confinement, the impurity position and the polaronic corrections. (author)

  13. Microsolvation effects on the electron binding energies of halide anions

    Science.gov (United States)

    Dolgounitcheva, O.; Zakrzewski, V. G.; Streit, L.; Ortiz, J. V.

    2014-02-01

    Ab initio electron propagator calculations in the partial third order (P3) and P3+ approximations were performed to obtain vertical electron detachment energies (VEDEs) of fluoride and chloride clusters with one through three molecules of water. Larger clusters of F- and Cl- with six water molecules were also treated with and without the polarisable continuum model (PCM). For the smaller clusters, good agreement between calculated VEDEs and peak positions in photoelectron spectra is achieved. Large shifts in VEDEs are observed for both hexameric fluoride-water and chloride-water complexes when the PCM is applied. Significant changes in coordination geometries about the chloride anion also occur in this model. In all fluoride complexes, Dyson orbitals for the lowest VEDEs are delocalised over oxygen atoms. On the contrary, for the case of chloride-water clusters, the Dyson orbitals corresponding to the lowest VEDEs are localised on the anion.

  14. Estimating binding free energy of a putative growth factors EGF-VEGF complex - a computational bioanalytical study.

    Science.gov (United States)

    Lin, Meng-Han; Chang, C Allen; Fischer, Wolfgang B

    2016-08-01

    Epidermal growth factor (EGF) and homodimeric vascular endothelial growth factor (VEGF) bind to cell surface receptors. They are responsible for cell growth and angiogenesis, respectively. Docking of the individual proteins as monomeric units using ZDOCK 2.3.2 reveals a partial blocking of the receptor binding site of VEGF by EGF. The receptor binding site of EGF is not affected by VEGF. The calculated binding energy is found to be intermediate between the binding energies calculated for Alzheimer's Aß42 and the barnase/barstar complex. PMID:26338536

  15. Alignment of RNA molecules: Binding energy and statistical properties of random sequences

    Energy Technology Data Exchange (ETDEWEB)

    Valba, O. V., E-mail: valbaolga@gmail.com [Moscow Institute of Physics and Technology (State University) (Russian Federation); Nechaev, S. K., E-mail: sergei.nechaev@gmail.com [Universite Paris Sud, LPTMS (France); Tamm, M. V., E-mail: thumm.m@gmail.com [Moscow State University (Russian Federation)

    2012-02-15

    A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energy between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.

  16. On the many-body Van der Waals binding energy of a dense fluid

    NARCIS (Netherlands)

    Nijboer, B.R.A.

    1975-01-01

    We consider a dense system of neutral atoms. When the atoms are represented by isotropic oscillators (Drude-Lorentz model) interacting with nonretarded dipole-dipole forces, the binding energy of the system is given exactly by a well-known expression which is written as a sum of two-bond, three-bond

  17. PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity.

    Science.gov (United States)

    Liu, Xiao; Liu, Jinfeng; Zhu, Tong; Zhang, Lujia; He, Xiao; Zhang, John Z H

    2016-05-23

    Improving the accuracy of scoring functions for estimating protein-ligand binding affinity is of significant interest as well as practical utility in drug discovery. In this work, PBSA_E, a new free energy estimator based on the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) descriptors, has been developed. This free energy estimator was optimized using high-quality experimental data from a training set consisting of 145 protein-ligand complexes. The method was validated on two separate test sets containing 121 and 130 complexes. Comparison of the binding affinities predicted using the present method with those obtained using three popular scoring functions, i.e., GlideXP, GlideSP, and SYBYL_F, demonstrated that the PBSA_E method is more accurate. This new energy estimator requires a MM/PBSA calculation of the protein-ligand binding energy for a single complex configuration, which is typically obtained by optimizing the crystal structure. The present study shows that PBSA_E has the potential to become a robust tool for more reliable estimation of protein-ligand binding affinity in structure-based drug design. PMID:27088302

  18. Photon Binding Energy during Self-trapping and filaments' Self-Organisation

    Science.gov (United States)

    Dantu, Subbarao; Uma, R.; Goyal, Sanjeev

    2000-10-01

    Self-trapping profiles of laser beams in one space dimension and in cylindrical geometry are obtained for saturating-type nonlinearities computationally. The relavant nonlinear Shrodinger equations are solved adjusting for the nonlinear wavenumber shifts till self-trapping is achieved.Note that in one space dimension case the self-trapping condition is the same as for soliton formation. The modelling of the self-trapped beams is done using an approximate gaussian ansatz. Self-consistency then demands that the refractive index profile be approximated by a suitable parabolic profile in space corresponding to two nearby turning points being present simultaneously. The estimation of the location of the turning points is accomplished by using the scheme of approximation on the refractive index in momentum space as suggested by Subbarao et.al.(Phys.Plasmas vol.5, pp.3440-3450 (1998)). This scheme automatically also suggests the method to estimate the per photon binding energy in the self-trapped beam that indicates the strength of self-trapping.The photon binding energy vs. the laser beam intensity is the required photon binding energy curve.Being so similar to the nuclear binding energy curve in shape, it also goes on to suggest how to accomplish more stable self-trapped structures by the fusion or fission of self-trapped filaments thereby giving rise to a new form of self-organisation.

  19. 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.

  20. 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)

  1. Determination of the Exciton Binding Energy Using Photothermal and Photoluminescence Spectroscopy

    Science.gov (United States)

    Strzałkowski, K.; Zakrzewski, J.; Maliński, M.

    2013-04-01

    In this paper, experimental photoluminescence (PL) and piezoelectric photothermal (PPT) spectra of selected II-VI binary crystals are presented and analyzed. The quantitative analysis of the photothermal spectra was performed using a modified and extended Jackson-Amer model. The values of the bandgap energies of investigated semiconductors were computed from the PT amplitude and phase spectra. From the temperature dependence of the exciton emission so-called "excitonic energy gaps" have been determined. It follows from the theory that the exciton binding energy is the difference of these two values of energy gaps derived from PPT and PL spectroscopy.

  2. Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin.

    Science.gov (United States)

    Koonammackal, Mathew Varghese; Nellipparambil, Unnikrishnan Viswambharan Nair; Sudarsanakumar, Chellappanpillai

    2011-11-01

    Curcumin is a natural phytochemical that exhibits a wide range of pharmacological properties, including antitumor and anticancer activities. The similarity in the shape of curcumin to DNA minor groove binding drugs is the motivation for exploring its binding affinity in the minor grooves of DNA sequences. Interactions of curcumin with DNA have not been extensively examined, while its pharmacological activities have been studied and documented in depth. Curcumin was docked with two DNA duplexes, d(GTATATAC)(2) and d(CGCGATATCGCG)(2), and molecular dynamics simulations of the complexes were performed in explicit solvent to determine the stability of the binding. In all systems, the curcumin is positioned in the minor groove in the A·T region, and was stably bound throughout the simulation, causing only minor modifications to the structural parameters of DNA. Water molecules were found to contribute to the stability of the binding of the ligand. Free energy analyses of the complexes were performed with MM-PBSA, and the binding affinities that were calculated are comparable to the values reported for other similar nucleic acid-ligand systems, indicating that curcumin is a suitable natural molecule for the development of minor groove binding drugs. PMID:21287216

  3. 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.

  4. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.

    Science.gov (United States)

    Duan, Li L; Feng, Guo Q; Zhang, Qing G

    2016-01-01

    Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding. PMID:27507430

  5. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

    Science.gov (United States)

    Duan, Li L.; Feng, Guo Q.; Zhang, Qing G.

    2016-01-01

    Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding. PMID:27507430

  6. The HSP90 binding mode of a radicicol-like E-oxime from docking, binding free energy estimations, and NMR 15N chemical shifts

    Science.gov (United States)

    Spichty, Martin; Taly, Antoine; Hagn, Franz; Kessler, Horst; Barluenga, Sofia; Winssinger, Nicolas; Karplus, Martin

    2009-01-01

    We determine the binding mode of a macrocyclic radicicol-like oxime to yeast HSP90 by combining computer simulations and experimental measurements. We sample the macrocyclic scaffold of the unbound ligand by parallel tempering simulations and dock the most populated conformations to yeast HSP90. Docking poses are then evaluated by the use of binding free energy estimations with the linear interaction energy method. Comparison of QM/MM-calculated NMR chemical shifts with experimental shift data for a selective subset of back-bone 15N provides an additional evaluation criteria. As a last test we check the binding modes against available structure-activity-relationships. We find that the most likely binding mode of the oxime to yeast HSP90 is very similar to the known structure of the radicicol-HSP90 complex. PMID:19482409

  7. Development of computational methods for the prediction of protein structure, protein binding, and mutational effects using free energy calculations.

    OpenAIRE

    Becker, Caroline

    2014-01-01

    A molecular understanding of protein-protein or protein-ligand binding is of crucial importance for the design of proteins or ligands with defined binding characteristics. The comprehensive analysis of biomolecular binding and the coupled rational in silico design of protein-ligand interfaces requires both, accurate and computationally fast methods for the prediction of free energies. Accurate free energy methods usually involve atomistic molecular dynamics simulations that are computationall...

  8. Free energy calculations to estimate ligand-binding affinities in structure-based drug design.

    Science.gov (United States)

    Reddy, M Rami; Reddy, C Ravikumar; Rathore, R S; Erion, Mark D; Aparoy, P; Reddy, R Nageswara; Reddanna, P

    2014-01-01

    Post-genomic era has led to the discovery of several new targets posing challenges for structure-based drug design efforts to identify lead compounds. Multiple computational methodologies exist to predict the high ranking hit/lead compounds. Among them, free energy methods provide the most accurate estimate of predicted binding affinity. Pathway-based Free Energy Perturbation (FEP), Thermodynamic Integration (TI) and Slow Growth (SG) as well as less rigorous end-point methods such as Linear interaction energy (LIE), Molecular Mechanics-Poisson Boltzmann./Generalized Born Surface Area (MM-PBSA/GBSA) and λ-dynamics have been applied to a variety of biologically relevant problems. The recent advances in free energy methods and their applications including the prediction of protein-ligand binding affinity for some of the important drug targets have been elaborated. Results using a recently developed Quantum Mechanics (QM)/Molecular Mechanics (MM) based Free Energy Perturbation (FEP) method, which has the potential to provide a very accurate estimation of binding affinities to date has been discussed. A case study for the optimization of inhibitors for the fructose 1,6- bisphosphatase inhibitors has been described. PMID:23947646

  9. Nuclear binding energies: Global collective structure and local shell-model correlations

    International Nuclear Information System (INIS)

    Nuclear binding energies and two-neutron separation energies are analysed starting from the liquid-drop model and the nuclear shell model in order to describe the global trends of the above observables. We subsequently concentrate on the Interacting Boson Model (IBM) and discuss a new method in order to provide a consistent description of both, ground-state and excited-state properties. We address the artefacts that appear when crossing mid-shell using the IBM formulation and perform detailed numerical calculations for nuclei situated in the 50-82 shell. We also concentrate on local deviations from the above global trends in binding energy and two-neutron separation energies that appear in the neutron-deficient Pb region. We address possible effects on the binding energy, caused by mixing of low-lying 0+ intruder states into the ground state, using configuration mixing in the IBM framework. We also study ground-state properties using a macroscopic-microscopic model. Detailed comparisons with recent experimental data in the Pb region are amply discussed

  10. Imaging G protein-coupled receptors while quantifying their ligand-binding free-energy landscape.

    Science.gov (United States)

    Alsteens, David; Pfreundschuh, Moritz; Zhang, Cheng; Spoerri, Patrizia M; Coughlin, Shaun R; Kobilka, Brian K; Müller, Daniel J

    2015-09-01

    Imaging native membrane receptors and testing how they interact with ligands is of fundamental interest in the life sciences but has proven remarkably difficult to accomplish. Here, we introduce an approach that uses force-distance curve-based atomic force microscopy to simultaneously image single native G protein-coupled receptors in membranes and quantify their dynamic binding strength to native and synthetic ligands. We measured kinetic and thermodynamic parameters for individual protease-activated receptor-1 (PAR1) molecules in the absence and presence of antagonists, and these measurements enabled us to describe PAR1's ligand-binding free-energy landscape with high accuracy. Our nanoscopic method opens an avenue to directly image and characterize ligand binding of native membrane receptors. PMID:26167642

  11. Analytical formulas for carrier density and Fermi energy in semiconductors with a tight-binding band

    International Nuclear Information System (INIS)

    Analytical formulas for evaluating the relation of carrier density and Fermi energy for semiconductors with a tight-binding band have been proposed. The series expansions for a carrier density with fast convergency have been obtained by means of a Bessel function. A simple and analytical formula for Fermi energy has been derived with the help of the Gauss integration method. The results of the proposed formulas are in good agreement with accurate numerical solutions. The formulas have been successfully used in the calculation of carrier density and Fermi energy in a miniband superlattice system. Their accuracy is in the order of 10−5. (paper)

  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. 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.

  14. 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.

  15. 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. PMID:27117350

  16. Binding Energies of D- Centers Trapped by a Quantum Dot in a Magnetic Field

    Institute of Scientific and Technical Information of China (English)

    XIE Wen-Fang

    2009-01-01

    A investigation of the properties of the bound states of D- centers confined in a parabolic quantum dot has been performed for the case with the presence of a perpendicular magnetic field.Calculations are carried out by using the method of numerical diagonalization of Hamiltonian matrix within the effective-mass approximation.The binding energies of the ground and some bound-excited states are obtained as a function of the applied magnetic field strength.Detailed calculations of the binding energies for a number of low-lying states show that for field strength less than B = 2.1 T, the D- center confined in a quantum dot possesses two bound states, for 2.1 ≤ B < 2.4 T, there exist three bound states, etc.Further relevant characteristics of the D- center quantum dots in magnetic fields are provided.

  17. Improved Computation of Protein-Protein Relative Binding Energies with the Nwat-MMGBSA Method.

    Science.gov (United States)

    Maffucci, Irene; Contini, Alessandro

    2016-09-26

    A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain number of explicit water molecules (Nwat) during the calculations, has been tested on a set of 20 protein-protein complexes, using the correlation between predicted and experimental binding energy as the evaluation metric. Besides the Nwat parameter, the effect of the force field, the molecular dynamics simulation length, and the implicit solvent model used in the MMGBSA analysis have been also evaluated. We found that considering 30 interfacial water molecules improved the correlation between predicted and experimental binding energies by up to 30%, compared to the standard approach. Moreover, the correlation resulted in being rather sensitive to the force field and, to a minor extent, to the implicit solvent model and to the length of the MD simulation. PMID:27500550

  18. 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.

  19. 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.

  20. Relationships between ligand binding sites, protein architecture and correlated paths of energy and conformational fluctuations

    International Nuclear Information System (INIS)

    The statistical thermodynamics basis of energy and residue position fluctuations is explained for native proteins. The protein and its surroundings are treated as a canonical system with emphasis on the effects of energy exchange between the two. Fluctuations of the energy are related to fluctuations of residue positions, which in turn are related to the connectivity matrix of the protein, thus establishing a connection between energy fluctuation pathways and protein architecture. The model gives the locations of hotspots for ligand binding and identifies the pathways of energy conduction within the protein. Results are discussed in terms of two sets of models, the BPTI and 12 proteins that contain the PDZ domain. A possible use of the model for determining functionally similar domains in a diverse set of proteins is pointed out

  1. 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.

  2. 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.

  3. 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.

  4. 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.

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

    Science.gov (United States)

    Nutho, Bodee; Khuntawee, Wasinee; Rungnim, Chompoonut; Pongsawasdi, Piamsook; Wolschann, Peter; Karpfen, Alfred; Kungwan, Nawee

    2014-01-01

    Summary 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. PMID:25550745

  6. 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.

  7. Binding energies of exciton complexes in transition metal dichalcogenide monolayers and effect of dielectric environment

    Science.gov (United States)

    Kylänpää, Ilkka; Komsa, Hannu-Pekka

    2015-11-01

    Excitons, trions, biexcitons, and exciton-trion complexes in two-dimensional transition metal dichalcogenide sheets of MoS2, MoSe2, MoTe2, WS2, and WSe2 are studied by means of density functional theory and path-integral Monte Carlo method in order to accurately account for the particle-particle correlations. In addition, the effect of dielectric environment on the properties of these exciton complexes is studied by modifying the effective interaction potential between particles. Calculated exciton and trion binding energies are consistent with previous experimental and computational studies, and larger systems such as biexciton and exciton-trion complex are found highly stable. Binding energies of biexcitons are similar to or higher than those of trions, but the binding energy of the trion depends significantly stronger on the dielectric environment than that of biexciton. Therefore, as a function of an increasing dielectric constant of the environment the exciton-trion complex "dissociates" to a biexciton rather than to an exciton and a trion.

  8. 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.

  9. Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.

    Science.gov (United States)

    Sulea, Traian; Vivcharuk, Victor; Corbeil, Christopher R; Deprez, Christophe; Purisima, Enrico O

    2016-07-25

    Affinity modulation of antibodies and antibody fragments of therapeutic value is often required in order to improve their clinical efficacies. Virtual affinity maturation has the potential to quickly focus on the critical hotspot residues without the combinatorial explosion problem of conventional display and library approaches. However, this requires a binding affinity scoring function that is capable of ranking single-point mutations of a starting antibody. We focus here on assessing the solvated interaction energy (SIE) function that was originally developed for and is widely applied to scoring of protein-ligand binding affinities. To this end, we assembled a structure-function data set called Single-Point Mutant Antibody Binding (SiPMAB) comprising several antibody-antigen systems suitable for this assessment, i.e., based on high-resolution crystal structures for the parent antibodies and coupled with high-quality binding affinity measurements for sets of single-point antibody mutants in each system. Using this data set, we tested the SIE function with several mutation protocols based on the popular methods SCWRL, Rosetta, and FoldX. We found that the SIE function coupled with a protocol limited to sampling only the mutated side chain can reasonably predict relative binding affinities with a Spearman rank-order correlation coefficient of about 0.6, outperforming more aggressive sampling protocols. Importantly, this performance is maintained for each of the seven system-specific component subsets as well as for other relevant subsets including non-alanine and charge-altering mutations. The transferability and enrichment in affinity-improving mutants can be further enhanced using consensus ranking over multiple methods, including the SIE, Talaris, and FOLDEF energy functions. The knowledge gained from this study can lead to successful prospective applications of virtual affinity maturation. PMID:27367467

  10. 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.

  11. A nonorthogonal tight-binding total energy model for molecular simulations

    International Nuclear Information System (INIS)

    A nonorthogonal tight-binding (TB) total energy model for molecular simulations has been developed in spirit of extended-Hueckel theory. The semiempirical potential parameters for H, C, O elements are fitted from density functional theory (DFT) calculations. The test calculations on small inorganic molecules, hydrocarbons, fullerenes, and large organic molecules show its reliability and transferability. In particular, the atomization energies and the gaps between highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO gaps) from TB model compare well with DFT results for a variety of molecules. Thus, our TB model can be used in the large scale simulation of molecules and carbon-based materials

  12. Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration.

    Science.gov (United States)

    Silver, Nathaniel W; King, Bracken M; Nalam, Madhavi N L; Cao, Hong; Ali, Akbar; Kiran Kumar Reddy, G S; Rana, Tariq M; Schiffer, Celia A; Tidor, Bruce

    2013-11-12

    Here we present a novel, end-point method using the dead-end-elimination and A* algorithms to efficiently and accurately calculate the change in free energy, enthalpy, and configurational entropy of binding for ligand-receptor association reactions. We apply the new approach to the binding of a series of human immunodeficiency virus (HIV-1) protease inhibitors to examine the effect ensemble reranking has on relative accuracy as well as to evaluate the role of the absolute and relative ligand configurational entropy losses upon binding in affinity differences for structurally related inhibitors. Our results suggest that most thermodynamic parameters can be estimated using only a small fraction of the full configurational space, and we see significant improvement in relative accuracy when using an ensemble versus single-conformer approach to ligand ranking. We also find that using approximate metrics based on the single-conformation enthalpy differences between the global minimum energy configuration in the bound as well as unbound states also correlates well with experiment. Using a novel, additive entropy expansion based on conditional mutual information, we also analyze the source of ligand configurational entropy loss upon binding in terms of both uncoupled per degree of freedom losses as well as changes in coupling between inhibitor degrees of freedom. We estimate entropic free energy losses of approximately +24 kcal/mol, 12 kcal/mol of which stems from loss of translational and rotational entropy. Coupling effects contribute only a small fraction to the overall entropy change (1-2 kcal/mol) but suggest differences in how inhibitor dihedral angles couple to each other in the bound versus unbound states. The importance of accounting for flexibility in drug optimization and design is also discussed.

  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. 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.``

  15. 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.

  16. Cellulose chain binding free energy drives the processive move of cellulases on the cellulose surface.

    Science.gov (United States)

    Wang, Yefei; Zhang, Shujun; Song, Xiangfei; Yao, Lishan

    2016-09-01

    Processivity is essential for cellulases in their catalysis of cellulose hydrolysis. But what drives the processive move is not well understood. In this work, we use Trichoderma reesei Cel7B as a model system and show that its processivity is directly correlated to the binding free energy difference of a cellulose chain occupying the binding sites -7 to +2 and that occupying sites -7 to -1. Several mutants that have stronger interactions with glycosyl units in sites +1 and +2 than the wild type enzyme show higher processivity. The results suggest that after the release of the product cellobiose located in sites +1 and +2, the enzyme pulls the cellulose chain to fill the vacant sites, which propels its processive move on the cellulose surface. Biotechnol. Bioeng. 2016;113: 1873-1880. © 2016 Wiley Periodicals, Inc. PMID:26928155

  17. 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.

  18. Constraining the gravitational binding energy of PSR J0737-3039B using terrestrial nuclear data

    International Nuclear Information System (INIS)

    We show that the gravitational binding energy of a neutron star of a given mass is correlated with the slope of the nuclear symmetry energy at 1-2 times nuclear saturation density for equations of state without significant softening (i.e., those that predict maximum masses Mmax>1.44M· in line with the largest accurately measured neutron star mass). Applying recent laboratory constraints on the slope of the symmetry energy to this correlation we extract a constraint on the baryon mass of the lower mass member of the double pulsar binary system, PSR J0737-3039B. We compare with independent constraints derived from modeling the progenitor star of J0737-3039B up to and through its collapse under the assumption that it formed in an electron capture supernova. The two sets of constraints are consistent only if L < or approx. 70 MeV.

  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. 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.

  1. Benchmark Theoretical Study of the π–π Binding Energy in the Benzene Dimer

    Energy Technology Data Exchange (ETDEWEB)

    Miliordos, Evangelos; Aprà, Edoardo; Xantheas, Sotiris S.

    2014-09-04

    We establish a new estimate for the binding energy between two benzene molecules in the parallel-displaced (PD) conformation by systematically converging (i) the intra- and intermolecular geometry at the minimum, (ii) the expansion of the orbital basis set, and (iii) the level of electron correlation. The calculations were performed at the second-order Møller–Plesset perturbation (MP2) and the coupled cluster including singles, doubles, and a perturbative estimate of triples replacement [CCSD(T)] levels of electronic structure theory. At both levels of theory, by including results corrected for basis set superposition error (BSSE), we have estimated the complete basis set (CBS) limit by employing the family of Dunning’s correlation-consistent polarized valence basis sets. The largest MP2 calculation was performed with the cc-pV6Z basis set (2772 basis functions), whereas the largest CCSD(T) calculation was with the cc-pV5Z basis set (1752 basis functions). The cluster geometries were optimized with basis sets up to quadruple-ζ quality, observing that both its intra- and intermolecular parts have practically converged with the triple-ζ quality sets. The use of converged geometries was found to play an important role for obtaining accurate estimates for the CBS limits. Our results demonstrate that the binding energies with the families of the plain (cc-pVnZ) and augmented (aug-cc-pVnZ) sets converge [within <0.01 kcal/mol for MP2 and <0.15 kcal/mol for CCSD(T)] to the same CBS limit. In addition, the average of the uncorrected and BSSE-corrected binding energies was found to converge to the same CBS limit much faster than either of the two constituents (uncorrected or BSSE-corrected binding energies). Due to the fact that the family of augmented basis sets (especially for the larger sets) causes serious linear dependency problems, the plain basis sets (for which no linear dependencies were found) are deemed as a more efficient and straightforward path for

  2. Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines.

    Science.gov (United States)

    Koppisetty, Chaitanya A K; Frank, Martin; Kemp, Graham J L; Nyholm, Per-Georg

    2013-10-28

    Computing binding energies of protein-ligand complexes including their enthalpy and entropy terms by means of computational methods is an appealing approach for selecting initial hits and for further optimization in early stages of drug discovery. Despite the importance, computational predictions of thermodynamic components have evaded attention and reasonable solutions. In this study, support vector machines are used for developing scoring functions to compute binding energies and their enthalpy and entropy components of protein-ligand complexes. The binding energies computed from our newly derived scoring functions have better Pearson's correlation coefficients with experimental data than previously reported scoring functions in benchmarks for protein-ligand complexes from the PDBBind database. The protein-ligand complexes with binding energies dominated by enthalpy or entropy term could be qualitatively classified by the newly derived scoring functions with high accuracy. Furthermore, it is found that the inclusion of comprehensive descriptors based on ligand properties in the scoring functions improved the accuracy of classification as well as the prediction of binding energies including their thermodynamic components. The prediction of binding energies including the enthalpy and entropy components using the support vector machine based scoring functions should be of value in the drug discovery process.

  3. 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.

  4. The binding energy of soliton molecules in dispersion-managed optical fibers

    International Nuclear Information System (INIS)

    Solitons in dispersion managed optical fibers can form stable bound states known as soliton molecules. In this work, a mathematical model based on the variational approximation has been proposed, which describes the propagation of soliton molecules in optical fibers. Analytic results are compared with numerical simulation of the nonlinear Schrodinger equation, and qualitative agreement between them is demonstrated. The advantage of the proposed model consists in the possibility to estimate the binding energy of solitons in the molecule and interpretation of the decay of a molecule into separate solitons. The results can be useful in the design of communication systems where optical solitons are employed as carriers of information. (authors)

  5. 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.

  6. Folding model analysis of Λ binding energies and three-body ΛNN force

    International Nuclear Information System (INIS)

    Working within the framework of the folding model, we analyze the Λ binding energy data of light hypernuclei with effective two-body ΛN plus three-body ΛNN interaction. The two-body density for the core nucleus required for evaluating the three-body force contribution is obtained in terms of the centre of mass pair correlation. It is found that except for Λ5He the data are fairly well explained. The three-body force seems to account for the density dependence of the effective two-body ΛN interaction proposed earlier. (author). 13 refs, 2 tabs

  7. Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study

    OpenAIRE

    Honarparvar, Bahareh; Pawar, Sachin A; Alves, Cláudio Nahum; Lameira, Jerônimo; Maguire, Glenn EM; José Rogério A. Silva; Govender, Thavendran; Kruger, Hendrik G.

    2015-01-01

    Background Novel pentacycloundecane (PCU)-lactone-CO-EAIS peptide inhibitors were designed, synthesized, and evaluated against wild-type C-South African (C-SA) HIV-1 protease. Three compounds are reported herein, two of which displayed IC50 values of less than 1.00 μM. A comparative MM-PB(GB)SA binding free energy of solvation values of PCU-lactam and lactone models and their enantiomers as well as the PCU-lactam-NH-EAIS and lactone-CO-EAIS peptide inhibitors and their corresponding diastereo...

  8. Accurate core-electron binding energy shifts from density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Takahata, Yuji, E-mail: taka@iqm.unicamp.b [Amazonas State University, School of Engineering, Av. Darcy Vargas, 1200, Parque 10 - CEP 69065-020, Manaus, Amazonas (Brazil); Department of Chemistry, University of Campinas-UNICAMP, Campinas 13084-862, Sao Paulo (Brazil); Marques, Alberto Dos Santos [Amazonas State University, School of Engineering, Av. Darcy Vargas, 1200, Parque 10 - CEP 69065-020, Manaus, Amazonas (Brazil)

    2010-05-15

    Current review covers description of density functional methods of calculation of accurate core-electron binding energy (CEBE) of second and third row atoms; applications of calculated CEBEs and CEBE shifts (DELTACEBEs) in elucidation of topics such as: hydrogen-bonding, peptide bond, polymers, DNA bases, Hammett substituent (sigma) constants, inductive and resonance effects, quantitative structure activity relationship (QSAR), and solid state effect (WD). This review limits itself to works of mainly Chong and his coworkers for the period post-2002. It is not a fully comprehensive account of the current state of the art.

  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. 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.

  11. A Thousand Invisible Cords Binding Astronomy and High-Energy Physics

    CERN Document Server

    Kolb, Edward W

    2007-01-01

    The traditional realm of astronomy is the observation and study of the largest objects in the Universe, while the traditional domain of high-energy physics is the study of the smallest things in nature. But these two sciences concerned with opposite ends of the size spectrum are, in Muir's words, bound fast by a thousand invisible cords that cannot be broken. In this essay I propose that collaborations of astronomers and high-energy physicists on common problems are beneficial for both fields, and that both astronomy and high-energy physics can advance by this close and still growing relationship. Dark matter and dark energy are two of the binding cords I will use to illustrate how collaborations of astronomers and high-energy physicists on large astronomical projects can be good for astronomy, and how discoveries in astronomy can guide high-energy physicists in their quest for understanding nature on the smallest scales. Of course, the fields have some different intellectual and collaborative traditions, nei...

  12. Using nonfluorescent Förster resonance energy transfer acceptors in protein binding studies.

    Science.gov (United States)

    Ruan, Qiaoqiao; Skinner, Joseph P; Tetin, Sergey Y

    2009-10-15

    The purpose of this article is to highlight the versatility of nonfluorescent Förster resonance energy transfer (FRET) acceptors in determination of protein equilibrium dissociation constants and kinetic rates. Using a nonfluorescent acceptor eliminates the necessity to spectrally isolate the donor fluorescence when performing binding titrations covering a broad range of reagent concentrations. Moreover, random distribution of the donor and acceptor chromophores on the surface of proteins increases the probability of FRET occurring on their interaction. Three high-affinity antibodies are presented in this study as characteristic protein systems. Monoclonal antibody (mAb) 106.3 binds brain natriuretic peptide (BNP)5-13(C10A) and full-length BNP1-32 with the dissociation constants 0.26+/-0.01 and 0.05+/-0.02 nM, respectively, which was confirmed by kinetic measurements. For anti-hCG (human chorionic gonadotropin) mAb 8F11, studied at two incorporation ratios (IRs=1.9 and 3.8) of the nonfluorescent FRET acceptor, K(D) values of 0.04+/-0.02 and 0.059(-0.004)(+0.006) nM, respectively, were obtained. Likewise, the binding of goat anti-hamster immunoglobulin G (IgG) antibody was not affected by conjugation and yielded K(D) values of 1.26+/-0.04, 1.25+/-0.05, and 1.14+/-0.04 nM at IRs of 1.7, 4.7, and 8.1, respectively. We conclude that this FRET-based method offers high sensitivity, practical simplicity, and versatility in protein binding studies. PMID:19563765

  13. 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...

  14. Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.

    Science.gov (United States)

    Manohar, Suresh; Mantz, Amber R; Bancroft, Kevin E; Hui, Chung-Yuen; Jagota, Anand; Vezenov, Dmitri V

    2008-12-01

    We measured the force required to peel single-stranded DNA molecules from single-crystal graphite using chemical force microscopy. Force traces during retraction of a tip chemically modified with oligonucleotides displayed characteristic plateaus with abrupt force jumps, which we interpreted as a steady state peeling process punctuated by complete detachment of one or more molecules. We were able to differentiate between bases in pyrimidine homopolymers; peeling forces were 85.3 - 4.7 pN for polythymine and 60.8 +/- 5.5 pN for polycytosine, substantially independent of salt concentration and the rate of detachment. We developed a model for peeling a freely jointed chain from the graphite surface and estimated the average binding energy per monomer to be 11.5 +/- 0.6 k(B)T and 8.3 +/- 0.7 k(B)T in the cases of thymine and cytosine nucleotides, respectively. The equilibrium free-energy profile simulated using molecular dynamics had a potential well of 18.9 k(B)T for thymidine, showing that nonelectrostatic interactions dominate the binding. The discrepancy between the experiment and theory indicates that not all bases are adsorbed on the surface or that there is a population of conformations in which they adsorb. Force spectroscopy using oligonucleotides covalently linked to AFM tips provides a flexible and unambiguous means to quantify the strength of interactions between DNA and a number of substrates, potentially including nanomaterials such as carbon nanotubes. PMID:19368004

  15. 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...

  16. 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.

  17. 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.

  18. Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Sheng, WC; Zhuang, ZB; Gao, MR; Zheng, J; Chen, JGG; Yan, YS

    2015-01-08

    The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearly increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.

  19. Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy

    Science.gov (United States)

    Sheng, Wenchao; Zhuang, Zhongbin; Gao, Minrui; Zheng, Jie; Chen, Jingguang G.; Yan, Yushan

    2015-01-01

    The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearly increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.

  20. 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

  1. 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.

  2. The impacts of electronic state hybridization on the binding energy of single phosphorus donor electrons in extremely downscaled silicon nanostructures

    Science.gov (United States)

    The Anh, Le; Moraru, Daniel; Manoharan, Muruganathan; Tabe, Michiharu; Mizuta, Hiroshi

    2014-08-01

    We present the density functional theory calculations of the binding energy of the Phosphorus (P) donor electrons in extremely downscaled single P-doped Silicon (Si) nanorods. In past studies, the binding energy of donor electrons was evaluated for the Si nanostructures as the difference between the ionization energy for the single P-doped Si nanostructures and the electron affinity for the un-doped Si nanostructures. This definition does not take into account the strong interaction of donor electron states and Si electron states explicitly at the conductive states and results in a monotonous increase in the binding energy by reducing the nanostructure's dimensions. In this paper, we introduce a new approach to evaluate the binding energy of donor electrons by combining the projected density of states (PDOS) analysis and three-dimensional analysis of associated electron wavefunctions. This enables us to clarify a gradual change of the spatial distribution of the 3D electron wavefunctions (3DWFs) from the donor electron ground state, which is fully localized around the P donor site to the first conductive state, which spreads over the outer Si nanorods contributing to current conduction. We found that the energy of the first conductive state is capped near the top of the atomistic effective potential at the donor site with respect to the surrounding Si atoms in nanorods smaller than about 27 a0. This results in the binding energy of approximately 1.5 eV, which is virtually independent on the nanorod's dimensions. This fact signifies a good tolerance of the binding energy, which governs the operating temperature of the single dopant-based transistors in practice. We also conducted the computationally heavy transmission calculations of the single P-doped Si nanorods connected to the source and drain electrodes. The calculated transmission spectra are discussed in comparison with the atomistic effective potential distributions and the PDOS-3DWFs method.

  3. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

    OpenAIRE

    Tanida, Yoshiaki; Ito, Masakatsu; Fujitani, Hideaki

    2007-01-01

    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J. Chem. Phys. ${\\bf 123}$, 084108 (2005)]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a ...

  4. Orbital momentum distributions and binding energies for the complete valence shell of molecular iodine

    International Nuclear Information System (INIS)

    The complete valence shell binding energy spectrum (8-43eV) of I2 has been measured by using electron momentum spectroscopy at 1000eV. The complete inner valence region, corresponding to ionization from the 10 σu and 10 σg orbitals, has been measured for the first time and shows extensive splitting of the ionization strength due to electron correlation effects in the ion. Many-body calculations using the Green's function method have been carried out and are compared with the data. Momentum distributions, measured in both the outer and inner valence regions, are compared with those given by SCF orbital wave functions calculated with a number of different basis sets. Computed orbital position and momentum density maps for oriented I2 molecules are discussed in comparison with the measured and calculated spherically averaged momentum distributions

  5. 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.

  6. 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.

  7. 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).

  8. Electronic structure and binding energy relaxation of ScZr atomic alloying

    Science.gov (United States)

    Bo, Maolin; Guo, Yongling; Yang, Xuexian; He, Junjie; Liu, Yonghui; Peng, Cheng; Huang, Yongli; Sun, Chang Q.

    2016-07-01

    We examined the combined effect of atomic under- and hetero-coordination on the bond relaxation and electronic binding energy of Sc, Zr, and ScZr alloying using a combination of the bond-order-length-strength (BOLS) correlation and density functional theory (DFT) calculations. Observations strongly emphasize the relevance of core-level shifts as reliable X-ray photoelectron spectroscopy experimental descriptors of core-shell catalysis reactivity, along with under-coordinated atoms in bimetallic transition metal systems. The BOLS-DFT method provides enhanced catalysis reactivity and detects surface and alloy configurations, opening up the possibility to investigate more complex systems with irregularly under- and hetero-coordinated atoms.

  9. 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.

  10. Binding energy of one [sup 4]He impurity in liquid [sup 3]He

    Energy Technology Data Exchange (ETDEWEB)

    Boronat, J. (Universitat Politecnica de Catalunya, Barcelona (Spain)); Saavedra, F.A. de; Buendia, E. (Universidad de Granola (Spain)); Polls, A. (Universitat de Barcelona (Spain))

    1994-02-01

    A variational microscopic calculation of the binding energy of a [sup 4]He impurity ([mu][sub I]) in homogeneous liquid [sup 3]He at zero temperature is presented. Starting on an extended Jastrow-Slater wave function including three-body correlations, the expression for [mu][sub I] is derived and the appropriated FHNC formalism for this problem is reviewed. In the framework of the Average Correlation Approximation (ACA), it is proved that it is possible to obtain the chemical potential of the impurity only from liquid [sup 3]He magnitudes with a good accuracy. The results are consistent with both a recent experimental determination of [mu][sub I] at zero pressure and the non-solubility of [sup 4]He in [sup 3]He. However, numerical uncertainties preclude a firm conclusion about the latter property.

  11. Experimental determination of the deuterium binding energy with vacancies in tungsten

    Science.gov (United States)

    Zibrov, M.; Ryabtsev, S.; Gasparyan, Yu.; Pisarev, A.

    2016-08-01

    Deuterium (D) interaction with vacancies in tungsten (W) was studied using thermal desorption spectroscopy (TDS). In order to obtain a TDS spectrum with a prominent peak corresponding to D release from vacancies, a special procedure comprising damaging of a recrystallized W sample by low fluences of 10 keV/D ions, its annealing, and subsequent low-energy ion implantation, was utilized. This experimental sequence was performed several times in series; the only difference was the TDS heating rate that varied in the range of 0.15-4 K/s. The sum of the D binding energy (Eb) with vacancies and the activation energy for D diffusion (ED) in W was then directly determined from the slope of the Arrhenius-like plot ln(β / Tm2) versus 1/Tm, where β - heating rate and Tm - position of the respective peak in the TDS spectrum. The determined value of Eb + ED was 1.56 ± 0.06 eV.

  12. 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.

  13. 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...

  14. 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

  15. Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods.

    Directory of Open Access Journals (Sweden)

    Shuhua Shi

    Full Text Available The p53-MDMX interaction has attracted extensive attention of anti-cancer drug development in recent years. This current work adopted molecular dynamics (MD simulations and cross-correlation analysis to investigate conformation changes of MDMX caused by inhibitor bindings. The obtained information indicates that the binding cleft of MDMX undergoes a large conformational change and the dynamic behavior of residues obviously change by the presence of different structural inhibitors. Two different methods of binding free energy predictions were employed to carry out a comparable insight into binding mechanisms of four inhibitors PMI, pDI, WK23 and WW8 to MDMX. The data show that the main factor controlling the inhibitor bindings to MDMX arises from van der Waals interactions. The binding free energies were further divided into contribution of each residue and the derived information gives a conclusion that the hydrophobic interactions, such as CH-CH, CH-π and π-π interactions, are responsible for the inhibitor associations with MDMX.

  16. Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods.

    Science.gov (United States)

    Shi, Shuhua; Zhang, Shaolong; Zhang, Qinggang

    2015-01-01

    The p53-MDMX interaction has attracted extensive attention of anti-cancer drug development in recent years. This current work adopted molecular dynamics (MD) simulations and cross-correlation analysis to investigate conformation changes of MDMX caused by inhibitor bindings. The obtained information indicates that the binding cleft of MDMX undergoes a large conformational change and the dynamic behavior of residues obviously change by the presence of different structural inhibitors. Two different methods of binding free energy predictions were employed to carry out a comparable insight into binding mechanisms of four inhibitors PMI, pDI, WK23 and WW8 to MDMX. The data show that the main factor controlling the inhibitor bindings to MDMX arises from van der Waals interactions. The binding free energies were further divided into contribution of each residue and the derived information gives a conclusion that the hydrophobic interactions, such as CH-CH, CH-π and π-π interactions, are responsible for the inhibitor associations with MDMX. PMID:26513747

  17. 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.

  18. Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.

    Science.gov (United States)

    Wu, Kuan-Wei; Chen, Po-Chin; Wang, Jun; Sun, Ying-Chieh

    2012-10-01

    In the present study, we carried out thermodynamic integration molecular dynamics simulation for a pair of analogous inhibitors binding with Erk kinase to investigate how computation performs in reproducing the relative binding free energy. The computation with BCC-AM1 charges for ligands gave -1.1 kcal/mol, deviated from experimental value of -2.3 kcal/mol by 1.2 kcal/mol, in good agreement with experimental result. The error of computed value was estimated to be 0.5 kcal/mol. To obtain convergence, switching vdw interaction on and off required approximately 10 times more CPU time than switching charges. Residue-based contributions and hydrogen bonding were analyzed and discussed. Furthermore, subsequent simulation using RESP charge for ligand gave ΔΔG of -1.6 kcal/mol. The computed results are better than the result of -5.6 kcal/mol estimated using PBSA method in a previous study. Based on these results, we further carried out computations to predict ΔΔG for five new analogs, focusing on placing polar and nonpolar functional groups at the meta site of benzene ring shown in the Fig. 1, to see if these ligands have better binding affinity than the above ligands. The computations resulted that a ligand with polar -OH group has better binding affinity than the previous examined ligand by ~2.0 kcal/mol and two other ligands have better affinity by ~1.0 kcal/mol. The predicted better inhibitors of this kind should be of interest to experimentalist for future experimental enzyme and/or cell assays. PMID:22986633

  19. 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.

  20. 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.

  1. Transitions, cross sections and neutron binding energy in 186Re by Prompt Gamma Activation Analysis

    Science.gov (United States)

    Lerch, A. G.; Hurst, A. M.; Firestone, R. B.; Revay, Zs.; Szentmiklosi, L.; McHale, S. R.; McClory, J. W.; Detwiler, B.; Carroll, J. J.

    2014-03-01

    The nuclide 186Re possesses an isomer with 200,000 year half-life while its ground state has a half-life of 3.718 days. It is also odd-odd and well-deformed nucleus, so should exhibit a variety of other interesting nuclear-structure phenomena. However, the available nuclear data is rather sparse; for example, the energy of the isomer is only known to within + 7 keV and, with the exception of the J?=1- ground state, every proposed level is tentative in the ENSDF. Previously, Prompt Gamma Activation Analysis (PGAA) was utilized to study natRe with 186,188Re being produced via thermal neutron capture. Recently, an enriched 185Re target was irradiated by thermal neutrons at the Budapest Research Reactor to build on those results. Prompt (primary and secondary) and delayed gamma-ray transitions were measured with a large-volume, Compton-suppressed HPGe detector. Absolute cross sections for each gamma transition were deduced and corrected for self attenuation within the sample. Fifty-two primary gamma-ray transitions were newly identified and used to determine a revised value of the neutron binding energy. DICEBOX was used to simulate the decay scheme and the total radiative thermal neutron capture cross section was found to be 97+/-3 b Supported by DTRA (Detwiler) through HDTRA1-08-1-0014.

  2. 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

  3. 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.

  4. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

    Energy Technology Data Exchange (ETDEWEB)

    Tanida, Yoshiaki [Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa (Japan)], E-mail: tanida@labs.fujitsu.com; Ito, Masakatsu; Fujitani, Hideaki [Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa (Japan)

    2007-08-16

    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C.D. Snow, M.R. Shirts, E.J. Sorin, V.S. Pande, J. Chem. Phys. 123 (2005) 084108]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant {lambda}, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies {delta}G thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda et al. [H. Gouda, I.D. Kuntz, D.A. Case, P.A. Kollman, Biopolymers 68 (2003) 16], the predictive accuracy of the relative values {delta}{delta}G is almost comparable to that of TI: the correlation coefficients (R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of {approx}-7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated.

  5. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

    Science.gov (United States)

    Tanida, Yoshiaki; Ito, Masakatsu; Fujitani, Hideaki

    2007-08-01

    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C.D. Snow, M.R. Shirts, E.J. Sorin, V.S. Pande, J. Chem. Phys. 123 (2005) 084108]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant λ, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies Δ G thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda et al. [H. Gouda, I.D. Kuntz, D.A. Case, P.A. Kollman, Biopolymers 68 (2003) 16], the predictive accuracy of the relative values ΔΔ G is almost comparable to that of TI: the correlation coefficients ( R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of ˜-7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated.

  6. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

    International Nuclear Information System (INIS)

    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C.D. Snow, M.R. Shirts, E.J. Sorin, V.S. Pande, J. Chem. Phys. 123 (2005) 084108]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant λ, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies ΔG thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda et al. [H. Gouda, I.D. Kuntz, D.A. Case, P.A. Kollman, Biopolymers 68 (2003) 16], the predictive accuracy of the relative values ΔΔG is almost comparable to that of TI: the correlation coefficients (R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of ∼-7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated

  7. 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.

  8. 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.

  9. 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.

  10. Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations.

    Science.gov (United States)

    Lu, Haiting; Huang, Xiaoqin; AbdulHameed, Mohamed Diwan M; Zhan, Chang-Guo

    2014-04-01

    Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been performed to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson-Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2A6-inhibitor binding affinity are two crucial internuclear distances, that is, the distance between the heme iron atom of CYP2A6 and the coordinating atom of the inhibitor, and the hydrogen-bonding distance between the N297 side chain of CYP2A6 and the pyridine nitrogen of the inhibitor. The combined MD simulations and QM/MM-PBSA calculations have led to dynamic CYP2A6-inhibitor binding structures that are consistent with the observed dynamic behaviors and structural features of CYP2A6-inhibitor binding, and led to the binding free energies that are in good agreement with the experimentally-derived binding free energies. The agreement between the calculated binding free energies and the experimentally-derived binding free energies suggests that the combined MD and QM/MM-PBSA approach may be used as a valuable tool to accurately predict the CYP2A6-inhibitor binding affinities in future computational design of new, potent and selective CYP2A6 inhibitors. PMID:24631364

  11. Electron momentum distributions and binding energies for the valence orbitals of hydrogen bromide and hydrogen iodide

    International Nuclear Information System (INIS)

    The electron binding energy spectra and momentum distributions have been obtained for the valence orbitals of HBr and HI using noncoplanar symmetric electron coincidence spectroscopy at 1200eV. The weakly bonding inner valence ns orbitals, which have not been previously observed, have their spectroscopic (pole) strength severely split among a number of ion states. For HBr the strength of the main inner valence (ns) transition is 0.42 0.03 whereas for HI it is 0.37 0.04, in close agreement with that observed for the valence s orbitals of the corresponding isoelectronic inert gas atoms. The spectroscopic strength for the two outermost orbitals is found to be close to unity, in agreement with many body Green's function calculations. The measured momentum distributions are compared with several spherically averaged MO momentum distributions, as well as (for HBr) with a Green's function calculation of the generalized overlap amplitude (GOA). The GOA momentum distributions are in excellent agreement with the HBr data, both in shape and relative magnitude. Not all of the MO momentum distributions are in reasonable agreement with the data. Comparison is also made with the calculated momentum distributions for Kr, Br, Xe and I

  12. Exciton Binding Energy in Organic-Inorganic Tri-Halide Perovskites.

    Science.gov (United States)

    Askar, Abdelrahman M; Shankar, Karthik

    2016-06-01

    The recent dramatic increase in the power conversion efficiencies of organic-inorganic tri-halide perovskite solar cells has triggered intense research worldwide and created a paradigm shift in the photovoltaics field. It is crucial to develop a solid understanding of the photophysical processes underlying solar cell operation in order to both further improve the photovoltaic performance of perovskite solar cells as well as to exploit the broader optoelectronic applications of the tri-halide perovskites. In this short review, we summarize the main research findings about the binding energy of excitons in tri-halide perovskite materials and find that a value in the range of 2-22 meV at room temperature would be a safe estimate. Spontaneous free carrier generation is the dominant process taking place directly after photoexcitation in organic-inorganic tri-halide perovskites at room temperature, which eliminates the exciton diffusion bottleneck present in organic solar cells and constitutes a major contributing factor to the high photovoltaic performance of this material. PMID:27427650

  13. Isotopic dependence of the nuclear charge radii and binding energies in the relativistic Hartree-Fock formalism

    Energy Technology Data Exchange (ETDEWEB)

    Niembro, R., E-mail: niembror@unican.es; Marcos, S.; Lopez-Quelle, M. [Universidad de Cantabria (Spain); Savushkin, L. N. [St. Petersburg University for Telecommunications (Russian Federation)

    2012-03-15

    Relativistic nonlinear models based on the Hartree and Hartree-Fock approximations, including the {sigma}, {omega}, {pi}, and {rho} mesons, are worked out to explore the behavior of the nuclear charge radii and the binding energies of several isotopic chains. We find a correlation between the magnitude of the anomalous kink effect (KE) in the Pb isotopic family and the compressibility modulus (K) of nuclear matter. The KE appears to be sensitive, in particular, to the mechanisms which control the K value. The influence of the symmetry energy on the Ca isotopic chain is also studied. The behavior of the charge radii of single-particle states for some special cases and its repercussion on the nuclear charge radius is analyzed. The effect of pairing correlations on the models improves considerably the quality of the results in both binding energy and KE.

  14. 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...

  15. Influence of position dependent effective mass on donor binding energy in square and V-shaped quantum wells in the presence of a magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Panahi, H., E-mail: t-panahi@guilan.ac.ir [Department of Physics, University of Guilan, 41335-1914 Rasht (Iran, Islamic Republic of); Golshahi, S. [Department of Physics, Rasht Branch, Islamic Azad University, Rasht (Iran, Islamic Republic of); Doostdar, M. [Department of Physics, University of Guilan, 41335-1914 Rasht (Iran, Islamic Republic of)

    2013-06-01

    In this paper we have calculated variationally the ground state binding energy of a hydrogenic donor impurity in square quantum well and V-shaped quantum well as a function of the well width in the presence of magnetic fields with both constant and position dependent effective mass. The wave function of electrons confined to donor impurity within the quantum well is considered as the two dimensional and three dimensional trial wave functions. It has been found that by increasing the well width, the binding energy decreases smoothly to bulk values while its steepness is sharper in square quantum well in comparison with V-shaped quantum well. Increasing the magnetic field leads to the enhancement of binding energy. At higher magnetic fields, by increasing the well width, binding energy tends to a constant value. The effect of position dependent effective mass on the enhancement of binding energy is more evident in comparison with constant effective mass one.

  16. Influence of position dependent effective mass on donor binding energy in square and V-shaped quantum wells in the presence of a magnetic field

    International Nuclear Information System (INIS)

    In this paper we have calculated variationally the ground state binding energy of a hydrogenic donor impurity in square quantum well and V-shaped quantum well as a function of the well width in the presence of magnetic fields with both constant and position dependent effective mass. The wave function of electrons confined to donor impurity within the quantum well is considered as the two dimensional and three dimensional trial wave functions. It has been found that by increasing the well width, the binding energy decreases smoothly to bulk values while its steepness is sharper in square quantum well in comparison with V-shaped quantum well. Increasing the magnetic field leads to the enhancement of binding energy. At higher magnetic fields, by increasing the well width, binding energy tends to a constant value. The effect of position dependent effective mass on the enhancement of binding energy is more evident in comparison with constant effective mass one

  17. Steric and allosteric effects of fatty acids on the binding of warfarin to human serum albumin revealed by molecular dynamics and free energy calculations.

    Science.gov (United States)

    Fujiwara, Shin-Ichi; Amisaki, Takashi

    2011-01-01

    Human serum albumin (HSA) binds with drugs and fatty acids (FAs). This study was initiated to elucidate the relationship between the warfarin binding affinity of HSA and the positions of bound FA molecules. Molecular dynamics simulations of 11 HSA-warfarin-myristate complexes were performed. HSA-warfarin binding free energy was then calculated for each of the complexes by the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method. The results indicated that the magnitude of the binding free energy was smaller in HSA-warfarin complexes that had 4 or more myristate molecules than in complexes with no myristate molecules. The unfavorable effect on the HSA-warfarin binding affinity was caused sterically by the binding of a myristate molecule to the FA binding site closest to the warfarin binding site. On the other hand, the magnitude of HSA-warfarin binding free energy was largest when 3 myristate molecules were bound to the high-affinity sites. The strongest HSA-warfarin binding was attributable to favorable entropic contribution related to larger atomic fluctuations of the amino acid residues at the warfarin binding site. In the binding of 2 myristate molecules to the sites with the highest and second-highest affinities, allosteric modulation that enhanced electrostatic interactions between warfarin and some of the amino acid residues around the warfarin binding site was observed. This study clarified the structural and energetic properties of steric/allosteric effects of FAs on the HSA-warfarin binding affinity and illustrated the approach to analyze protein-ligand interactions in situations such that multiple ligands bind to the other sites of the protein. PMID:21720037

  18. Shedding Light on the EOS-Gravity Degeneracy and Constraining the Nuclear Symmetry Energy from the Gravitational Binding Energy of Neutron Stars

    OpenAIRE

    He Xiao-Tao; Fattoyev F. J.; Li Bao-An; Newton W. G.

    2016-01-01

    A thorough understanding of properties of neutron stars requires both a reliable knowledge of the equation of state (EOS) of super-dense nuclear matter and the strong-field gravity theories simultaneously. To provide information that may help break this EOS-gravity degeneracy, we investigate effects of nuclear symmetry energy on the gravitational binding energy of neutron stars within GR and the scalar-tensor subset of alternative gravity models. We focus on effects of the slope $L$ of nuclea...

  19. 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.

  20. Influence of geometrical factor on binding energy of Cooper pairs in YBa2Cu3O7-δ compound

    Science.gov (United States)

    Ibrahim, Saeed O.; Mustafa, Bassam M.

    2016-03-01

    In this research the influence of geometrical factors on binding energy between Cooper pairs are investigated for the high temperature superconducting (YBa2Cu3O7-δ) compound. This is done by using a model considering that the formation of Cooper pairs happens during tunneling mechanism of holes between the two CuO2 layers in the YBCO crystal which are considered as forming adjacent ridged potential wells. According to this model binding energy is: Eb i n=4/√{2 }m3/2 π2ħ3p ×∫U-0(U -0-E) exp [-2/(d -Rc) ħ √{2 m (U -E ) } ] √{E } d E 0 is a work function, ħ is the Plank's constant, m is the electron mass, and U is the height of the potential barrier, E is the energy, Rc is the electron cloud radius in tunneling direction and d is the distance between the two CuO2 planes. In the above model two effects of geometrical factors were ignored, considering that ridges in the two CuO2 layers as having rectangular shape, but in reality the ridges in the potential well are of triangular shape. Also the model considers the distance between layers as constant but really the distant d is variable due to the triangular geometry. In this work we consider both effects that affect the density of state in the potential well and the tunneling probability. Then binding energy between the Cooper pairs, is calculated.

  1. 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.

  2. 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)

  3. 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.

  4. 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.

  5. Binding Energy of Positively and Negatively Charged Excitons in GaAs/AlxGal-xAs Quantum Wells

    Institute of Scientific and Technical Information of China (English)

    刘建军; 张淑芳; 杨国琛; 李树深

    2002-01-01

    Using a simple two-parameter wavefunction, we calculate variationally the binding energy of positively and negatively charged excitons in GaAs/AlxGa1-xAs quantum wells for well widths from 10 to 300A. We consider the effect of effective mass, dielectric constant mismatch in the two materials, and the whole correlation among the particles. The results are discussed and compared in detail with previous experimental and theoretical results,which show fair agreement with them.

  6. A New Model for Calculating the Binding Energy of Lithium Nucleus under the Generalized Yukawa Potential and Hellmann Potential

    OpenAIRE

    Ghazvini, M; Salehi, N; Rajabi, A. A.

    2014-01-01

    In this paper, the Schr\\"odinger equation for 6-body system is studied. We solved this equation for lithium nucleus by using supersymmetry method with the specific potentials. These potentials are Yukawa potential, the generalized Yukawa potential and Hellmann potential. The results of our model for all calculations show that the ground state binding energy of Lithium nucleus with these potentials are very close to the ones obtained in experiments.

  7. The effect of Fermi momentum cutoff on the binding energy of closed-shell nuclei in the LOCV framework

    International Nuclear Information System (INIS)

    The ground-state binding energies of the light symmetric closed-shell nuclei, i.e., 4He, 12C, 16O and 40Ca, and the heavy asymmetric ones, i.e., 48Ca, 90Zr and 120Sn, are calculated in the harmonic oscillator (HOS) basis, by imposing the relative Fermi momentum cutoff of two point-like interacting nucleons on the density-dependent average effective interactions (DDAEI). The DDAEI are generated through the lowest order constrained variational (LOCV) method calculations for the asymmetric nuclear matter with the operator and the channel-dependent-type bare nucleon-nucleon potentials, such as the Argonne Av18jmax=2 and the Reid soft core, Reid68, interactions. In the framework of the harmonic oscillator shell model, the cutoff is imposed by defining the maximum value of the relative quantum numbers (RQNmax) in two ways: (1) the RQNmax of the last shell and (2) the RQNmax of each shell, in the ground state of the nucleus. It is shown that present results on the binding energies and the root-mean-square radius are closer to the corresponding experimental data than our previous works with the same DDAEI potentials, but without the cutoff constraint. However, for the light symmetric nuclei, the second scheme gives less binding energy and larger root-mean-square radius compared to the first one, while the situation is reversed for the heavier nuclei.

  8. Configuration space method for calculating binding energies of exciton complexes in quasi-1D/2D semiconductors

    Science.gov (United States)

    Bondarev, Igor

    A configuration space method, pioneered by Landau and Herring in studies of molecular binding and magnetism, is developed to obtain universal asymptotic relations for lowest energy exciton complexes (trion, biexciton) in confined semiconductor nanostructures such as nanowires and nanotubes, as well as coupled quantum wells. Trions are shown to be more stable (have greater binding energy) than biexcitons in strongly confined quasi-1D structures with small reduced electron-hole masses. Biexcitons are more stable in less confined quasi-1D structures with large reduced electron-hole masses. The theory predicts a crossover behavior, whereby trions become less stable than biexcitons as the transverse size of the quasi-1D nanostructure increases, which might be observed on semiconducting carbon nanotubes of increasing diameters. This method is also efficient in calculating binding energies for trion-type electron-hole complexes formed by indirect excitons in double coupled quantum wells, quasi-2D nanostructures that show new interesting electroabsorption/refraction phenomena. Supported by DOE-DE-SC0007117.

  9. 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.

  10. Shedding Light on the EOS-Gravity Degeneracy and Constraining the Nuclear Symmetry Energy from the Gravitational Binding Energy of Neutron Stars

    CERN Document Server

    He, Xiao-Tao; Li, Bao-An; Newton, W G

    2015-01-01

    A thorough understanding of properties of neutron stars requires both a reliable knowledge of the equation of state (EOS) of super-dense nuclear matter and the strong-field gravity theories simultaneously. To provide information that may help break this EOS-gravity degeneracy, we investigate effects of nuclear symmetry energy on the gravitational binding energy of neutron stars within GR and the scalar-tensor subset of alternative gravity models. We focus on effects of the slope $L$ of nuclear symmetry energy at saturation density and the high-density behavior of nuclear symmetry energy. We find that the variation of either the density slope $L$ or the high-density behavior of nuclear symmetry energy leads to large changes in the binding energy of neutron stars. The difference in predictions using the GR and the scalar-tensor theory appears only for massive neutron stars, and even then is significantly smaller than the difference resulting from variations in the symmetry energy.

  11. Toward an Accurate and Inexpensive Estimation of CCSD(T)/CBS Binding Energies of Large Water Clusters.

    Science.gov (United States)

    Sahu, Nityananda; Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R

    2016-07-21

    Owing to the steep scaling behavior, highly accurate CCSD(T) calculations, the contemporary gold standard of quantum chemistry, are prohibitively difficult for moderate- and large-sized water clusters even with the high-end hardware. The molecular tailoring approach (MTA), a fragmentation-based technique is found to be useful for enabling such high-level ab initio calculations. The present work reports the CCSD(T) level binding energies of many low-lying isomers of large (H2O)n (n = 16, 17, and 25) clusters employing aug-cc-pVDZ and aug-cc-pVTZ basis sets within the MTA framework. Accurate estimation of the CCSD(T) level binding energies [within 0.3 kcal/mol of the respective full calculation (FC) results] is achieved after effecting the grafting procedure, a protocol for minimizing the errors in the MTA-derived energies arising due to the approximate nature of MTA. The CCSD(T) level grafting procedure presented here hinges upon the well-known fact that the MP2 method, which scales as O(N(5)), can be a suitable starting point for approximating to the highly accurate CCSD(T) [that scale as O(N(7))] energies. On account of the requirement of only an MP2-level FC on the entire cluster, the current methodology ultimately leads to a cost-effective solution for the CCSD(T) level accurate binding energies of large-sized water clusters even at the complete basis set limit utilizing off-the-shelf hardware. PMID:27351269

  12. Estimation of individual binding energies in some dimers involving multiple hydrogen bonds using topological properties of electron charge density

    Energy Technology Data Exchange (ETDEWEB)

    Ebrahimi, A., E-mail: Ebrahimi@hamoon.usb.ac.ir [Department of Chemistry, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan (Iran, Islamic Republic of); Habibi Khorassani, S.M.; Delarami, H. [Department of Chemistry, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan (Iran, Islamic Republic of)

    2009-11-18

    Individual hydrogen bond (HB) energies have been estimated in several systems involving multiple HBs such as adenine-thymine and guanine-cytosine using electron charge densities calculated at X...H hydrogen bond critical points (HBCPs) by atoms in molecules (AIM) method at B3LYP/6-311++G** and MP2/6-311++G** levels. A symmetrical system with two identical H bonds has been selected to search for simple relations between {rho}{sub HBCP} and individual E{sub HB}. Correlation coefficient between E{sub HB} and {rho}{sub HBCP} in the base of linear, quadratic, and exponential equations are acceptable and equal to 0.95. The estimated individual binding energies E{sub HB} are in good agreement with the results of atom-replacement approach and natural bond orbital analysis (NBO). The E{sub HB} values estimated from {rho} values at H...X BCP are in satisfactory agreement with the main geometrical parameter H...X. With respect to the obtained individual binding energies, the strength of a HB depends on the substituent and the cooperative effects of other HBs.

  13. Application of object-oriented programming in a time-dependent density-functional theory calculation of exciton binding energies

    CERN Document Server

    Yang, Zeng-hui

    2013-01-01

    This paper discusses the benefits of object-oriented programming to scientific computing, using our recent calculations of exciton binding energies with time-dependent density-functional theory (arXiv: 1302.6972) as a case study. We find that an object-oriented approach greatly facilitates the development, the debugging, and the future extension of the code by promoting code reusing. We show that parallelism is added easily in our code in a object-oriented fashion with ScaLAPACK, Boost::MPI and OpenMP.

  14. Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: Harmonic constraints for methanol dimer

    Energy Technology Data Exchange (ETDEWEB)

    Heger, Matthias; Suhm, Martin A.; Mata, Ricardo A., E-mail: rmata@gwdg.de [Georg-August-Universität Göttingen, Institut für Physikalische Chemie, Tammannstr. 6, 37077 Göttingen (Germany)

    2014-09-14

    The discrepancy between experimental and harmonically predicted shifts of the OH stretching fundamental of methanol upon hydrogen bonding to a second methanol unit is too large to be blamed mostly on diagonal and off-diagonal anharmonicity corrections. It is shown that a decisive contribution comes from post-MP2 electron correlation effects, which appear not to be captured by any of the popular density functionals. We also identify that the major deficiency is in the description of the donor OH bond. Together with estimates for the electronic and harmonically zero-point corrected dimer binding energies, this work provides essential constraints for a quantitative description of this simple hydrogen bond. The spectroscopic dissociation energy is predicted to be larger than 18 kJ/mol and the harmonic OH-stretching fundamental shifts by about −121 cm{sup −1} upon dimerization, somewhat more than in the anharmonic experiment (−111 cm{sup −1})

  15. Measurement of the minimum binding energy of the 2p sigma molecular orbital formed in heavy ion collisions

    International Nuclear Information System (INIS)

    In order to study the minimum 2p sigma binding energy and its collision broadening, a copper ion beam was extracted from the Cs-sputter source and accelerated by the EN-tandem at Western Michigan University. Copper beams of ten different energies between 3 and 56 MeV were directed onto a pure thin (approx. 50μg) and a pure thick (approx. 5 mg) copper target. The x-rays emitted under 900 were reduced in intensity with an 11 mil thick pure aluminum absorber and observed with an 80mm2 Si(Li) detector. We were able to obtain quite intense 2p sigma MO-spectra with Cu-beams as slow as 3, 4, 5 and 7 MeV for thick as well as the thin targets

  16. 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.

  17. 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....

  18. Binding energy of adsorbates on a noble-metal surface: exchange and correlation effects.

    Science.gov (United States)

    Rohlfing, Michael; Bredow, Thomas

    2008-12-31

    We discuss the adsorption of xenon and of PTCDA on the silver (111) surface within a first-principles approach, focusing on the adsorbate-substrate interaction energy as a function of distance. We combine exact exchange with correlation energy from the adiabatic-connection fluctuation-dissipation theorem. At a large distance Z from the surface, the correlation causes a van der Waals attraction [approximately -C3/(Z - Z0)3]. At a closer distance, the attraction deviates from its asymptotic form and, combined with the repulsive exact-exchange energy, yields an equilibrium in close agreement with experiment. PMID:19437654

  19. 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

    2016-09-28

    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. PMID:27452185

  20. 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.

  1. Binding energy and momentum distribution of nuclear matter using Green's function methods

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, A. (TRIUMF, 4004 Wesbrook Mall, Vancouver, British Columbia, Canada V6T 2A3 (CA)); Dickhoff, W.H. (Department of Physics, Washington University, St. Louis, Missouri 63130 (USA)); Polls, A. (Departament d' Estructura i Constituents de la Materia, Universitat de Barcelona, E-08028 Barcelona, Spain (ES))

    1991-05-01

    The influence of hole-hole (h-h) propagation in addition to the conventional particle-particle (p-p) propagation, on the energy per particle and the momentum distribution is investigated for the {ital v}{sub 2} central interaction which is derived from Reid's soft-core potential. The results are compared to Brueckner-Hartree-Fock calculations with a continuous choice for the single-particle (SP) spectrum. Calculation of the energy from a self-consistently determined SP spectrum leads to a lower saturation density. This result is not corroborated by calculating the energy from the hole spectral function, which is, however, not self-consistent. A generalization of previous calculations of the momentum distribution, based on a Goldstone diagram expansion, is introduced that allows the inclusion of h-h contributions to all orders. From this result an alternative calculation of the kinetic energy is obtained. In addition, a direct calculation of the potential energy is presented which is obtained from a solution of the ladder equation containing p-p and h-h propagation to all orders. These results can be considered as the contributions of selected Goldstone diagrams (including p-p and h-h terms on the same footing) to the kinetic and potential energy in which the SP energy is given by the quasiparticle energy. The results for the summation of Goldstone diagrams leads to a different momentum distribution than the one obtained from integrating the hole spectral function which in general gives less depletion of the Fermi sea. Various arguments, based partly on the results that are obtained, are put forward that a self-consistent determination of the spectral functions including the p-p and h-h ladder contributions (using a realistic interaction) will shed light on the question of nuclear saturation at a nonrelativistic level that is consistent with the observed depletion of SP orbitals in finite nuclei.

  2. Binding Free Energies for Nicotine Analogs Inhibiting Cytochrome P450 2A6 by a Combined Use of Molecular Dynamics Simulations and QM/MM-PBSA Calculations

    OpenAIRE

    Lu, Haiting; Huang, Xiaoqin; AbdulHameed, Mohamed Diwan M.; Zhan, Chang-Guo

    2014-01-01

    Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been perforemd to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson-Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2...

  3. 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

  4. Halide Binding and Inhibition of Laccase Copper Clusters: The Role of Reorganization Energy

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2015-01-01

    complicate characterization. Understanding these processes at the molecular level is thus desirable but theoretically unexplored. This paper reports systematic calculations of geometries, reorganization energies, and ionization energies for all partly oxidized states of the trinuclear copper clusters...... in realistic models with similar to 200 atoms. Corrections for scalar-relativistic effects, dispersion, and thermal effects were estimated. Fluoride, chloride, hydroxide, or water was bound to the T2 copper site of the oxidized resting state, and the peroxo intermediate was also computed for reference...

  5. Optical determination of phosphorus acceptor binding energy in bulk wide-gap II-VI semimagnetic semiconductors

    International Nuclear Information System (INIS)

    Zn1-xMnxTe and Cd1-xMnxTe semimagnetic semiconductors doped with phosphorus have been investigated by means of the resistivity, Hall effect, photoluminescence and reflectance measurements. The high p-type doping level of these materials was achieved using Zn3P2 and CdP2 as the sources of P-impurities. By applying a unique technology of high-pressure annealing we were able to overcome a self-compensation in Zn1-xMnxTe:P. As a result, the sample with high and controllable concentration of electrical active acceptors were produced. The ground state binding energy of phosphorus acceptors in both Zn1-xMnxTe and Cd1-xMnxTe as well as its variation with the phosphorus doping level were optically determined. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  6. Orbital momentum distribution and binding energies for the complete valence shell of molecular chlorine by electron momentum spectroscopy

    International Nuclear Information System (INIS)

    The complete valence shell binding energy spectrum (10-50 eV) of Cl2 has been determined using electron momentum (binary (e,2e)) spectroscopy. The inner valence region, corresponding to 4σu and 4σg ionization, has been measured for the first time and shows extensive splitting of the ionization strength due to electron correlation effects. These measurements are compared with the results of many-body calculations using Green's function and CI methods employing unpolarised as well as polarised wave functions. Momentum distributions, measured in both the outer and inner valence regions, are compared with calculations using a range of unpolarised and polarised wave functions. Computed orbital density maps in momentum and position space for oriented Cl2 molecules are discussed in comparison with the measured and calculated spherically averaged momentum distributions

  7. THE GENERALIZED RIEMANN PROBLEM FOR A SCALAR NONCONVEX COMBUSTION MODEL-THE PERTURBATION ON INITIAL BINDING ENERGY

    Institute of Scientific and Technical Information of China (English)

    Pan Lijun; Sheng Wancheng

    2012-01-01

    In this article,we study the generalized Riemann problem for a scalar nonconvex Chapman-Jouguet combustion model in a neighborhood of the origin (t > 0) on the (x,t) plane.We focus our attention to the perturbation on initial binding energy.The solutions are obtained constructively under the entropy conditions.It can be found that the solutions are essentially different from the corresponding Piemann solutions for some cases.Especially,two important phenomena are observed:the transition from detonation to deflagration followed by a shock,which appears in the numerical simulations [7,27]; the transition from deflagration to detonation (DDT),which is one of the core problems in gas dynamic combustion.

  8. Simulation investigations in the binding energy and mechanical properties of HMX-based polymer-bonded explosives

    Institute of Scientific and Technical Information of China (English)

    XIAO Jijun; FANG Guoyong; JI Guangfu; XIAO Heming

    2005-01-01

    The molecular simulations of the well-known high explosive β-HMX (cyclotetramethylene tetranitramine) and its fluorine containing polymer-bonded explosives (PBXs) were carried out with the combination method of quantum mechanics, molecular mechanics and molecular dynamics. The atomic cluster model, containing the β-HMX molecule and the polymer molecule whose chain dimension was about the same as β-HMX's, was fully optimized by AM1 and PM3 semi-empirical molecular orbital and molecular mechanical methods using COMPASS and PCFF force field. Then the calculated binding energy is found to be linearly correlated to each other. Molecular dynamics simulations using COMPASS force field were performed for β-HMX crystal and the PBXs involving β-HMX and a series of fluorine containing polymers. Their elastic coefficients, moduli and Poisson's ratios were calculated. It is found that the mechanical properties of β-HMX can be effectively improved by blending with fluorine containing polymers in small amounts.

  9. 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.

  10. 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.

  11. Study of quark mass dependence of binding energy for light nuclei in 2+1 flavor lattice QCD

    CERN Document Server

    Yamazaki, Takeshi; Kuramashi, Yoshinobu; Ukawa, Akira

    2015-01-01

    We investigate the formation of light nuclei with the nuclear mass number less than or equal to four in 2+1 flavor QCD using a non-perturbative improved Wilson quark and Iwasaki gauge actions. The quark mass is decreased from our previous work to the one corresponding to the pion mass of 0.30 GeV. In each multi-nucleon channel, the energy shift of the ground state relative to the assembly of free nucleons is calculated on two volumes, whose spatial extents are 4.3 fm and 5.8 fm. From the volume dependence of the energy shift, we distinguish a bound state of multi nucleons from an attractive scattering state. We find that all the ground states measured in this calculation are bound states. As in the previous studies at larger $m_\\pi$, our result indicates that at $m_\\pi = 0.30$ GeV the effective interaction between nucleons in the light nuclei is relatively stronger than the one in nature, since the results for the binding energies are larger than the experimental values and a bound state appears in the dineut...

  12. Size-dependent stability toward dissociation and ligand binding energies of phosphine-ligated gold cluster ions

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Grant E.; Priest, Thomas A.; Laskin, Julia

    2014-01-01

    The stability of sub-nanometer size gold clusters ligated with organic molecules is of paramount importance to the scalable synthesis of monodisperse size-selected metal clusters with highly tunable chemical and physical properties. For the first time, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) equipped with surface induced dissociation (SID) has been employed to investigate the time and collision energy resolved fragmentation behavior of cationic doubly charged gold clusters containing 7-9 gold atoms and 6-7 triphenylphosphine (TPP) ligands prepared by reduction synthesis in solution. The TPP ligated gold clusters are demonstrated to fragment through three primary dissociation pathways: (1) Loss of a neutral TPP ligand from the precursor gold cluster, (2) asymmetric fission and (3) symmetric fission and charge separation of the gold core resulting in formation of complementary pairs of singly charged fragment ions. Threshold energies and activation entropies of these fragmentation pathways have been determined employing Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental SID data. It is demonstrated that the doubly charged cluster ion containing eight gold atoms and six TPP ligands, (8,6)2+, exhibits exceptional stability compared to the other cationic gold clusters examined in this study due to its large ligand binding energy of 1.76 eV. Our findings demonstrate the dramatic effect of the size and extent of ligation on the gas-phase stability and preferred fragmentation pathways of small TPP-ligated gold clusters.

  13. Accurate computations of the structures and binding energies of the imidazole⋯benzene and pyrrole⋯benzene complexes

    Energy Technology Data Exchange (ETDEWEB)

    Ahnen, Sandra; Hehn, Anna-Sophia [Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe (Germany); Vogiatzis, Konstantinos D. [Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe (Germany); Center for Functional Nanostructures, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Straße 1a, D-76131 Karlsruhe (Germany); Trachsel, Maria A.; Leutwyler, Samuel [Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern (Switzerland); Klopper, Wim, E-mail: klopper@kit.edu [Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe (Germany); Center for Functional Nanostructures, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Straße 1a, D-76131 Karlsruhe (Germany)

    2014-09-30

    Highlights: • We have computed accurate binding energies of two NH⋯π hydrogen bonds. • We compare to results from dispersion-corrected density-functional theory. • A double-hybrid functional with explicit correlation has been proposed. • First results of explicitly-correlated ring-coupled-cluster theory are presented. • A double-hybrid functional with random-phase approximation is investigated. - Abstract: Using explicitly-correlated coupled-cluster theory with single and double excitations, the intermolecular distances and interaction energies of the T-shaped imidazole⋯benzene and pyrrole⋯benzene complexes have been computed in a large augmented correlation-consistent quadruple-zeta basis set, adding also corrections for connected triple excitations and remaining basis-set-superposition errors. The results of these computations are used to assess other methods such as Møller–Plesset perturbation theory (MP2), spin-component-scaled MP2 theory, dispersion-weighted MP2 theory, interference-corrected explicitly-correlated MP2 theory, dispersion-corrected double-hybrid density-functional theory (DFT), DFT-based symmetry-adapted perturbation theory, the random-phase approximation, explicitly-correlated ring-coupled-cluster-doubles theory, and double-hybrid DFT with a correlation energy computed in the random-phase approximation.

  14. 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 ...

  15. Exactly solvable tight-binding model on the RAN: fractal energy spectrum and Bose–Einstein condensation

    International Nuclear Information System (INIS)

    The Regularized Apollonian Network (RAN) is defined starting from a tetrahedral structure with four nodes all connected (generation 0). At any successive generations, new nodes are added and connected with the surrounding three nodes. As a result, a power-law cumulative distribution of connectivity P(k) ∝ 1/k η with η = ln(3)/ln(2) ≈ 1.585 is obtained. We initially consider a single-particle tight-binding model on the RAN. The eigenvalues of the Hamiltonian are exactly computed by a recursive approach for any size of the network. In the infinite size limit, the density of states and the cumulative distribution of states (integrated density of states) are also exactly determined. The relevant scaling behavior of the cumulative distribution close to the band bottom is shown to be a power law with an exponent depending on the spectral dimension and not on the dimension of the embedding space. We then consider a gas made by an infinite number of non-interacting bosons, each of them described by the tight-binding Hamiltonian on the RAN and we prove that, for sufficiently large bosonic density and sufficiently small temperature, a macroscopic fraction of the particles occupies the lowest single-particle energy state forming the Bose–Einstein condensate. Not only do we determine the transition temperature as a function of the bosonic density, but also the fraction of condensed particles, the fugacity, the energy and the specific heat for any temperature and bosonic density. (paper)

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

    International Nuclear Information System (INIS)

    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

  17. 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.

  18. Binding energies and scattering observables in the $^{4}He_{3}$ atomic system

    CERN Document Server

    Motovilov, A K; Sofianos, S A; Kolganova, E A

    2001-01-01

    The $^4$He$_3$ bound states and the scattering of a $^4$He atom off a $^4$He dimer at ultra-low energies are investigated using a hard-core version of the Faddeev differential equations. Various realistic $^4$He-$^4$He interactions were employed, amomg them the LM2M2 potential by Aziz and Slaman and the recent TTY potential by Tang, Toennies and Yiu. The ground state and the excited (Efimov) state obtained are compared with other results. The scattering lengths and the atom-diatom phase shifts were calculated for center of mass energies up to 2.45 mK. It was found that the LM2M2 and TTY potentials, although of quite different structure, give practically the same bound-state and scattering results.

  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. 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.

  1. 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.

  2. A Simple Efficient Method for Obtaining the Binding Energy of Lithium Nucleus under the Hulth\\'en and Inversely Quadratic Yukawa Potentials

    CERN Document Server

    Salehi, Nasrin

    2015-01-01

    In this paper, the binding energy of Lithium nucleus in a nonrelativistic model is obtained for the Hulth\\'en and the Inversely Quadratic Yukawa Potential. In order to that, we used the concept of supersymmetry to solving the Schr\\"odinger equation exact analytically. These potentials, due to their physical interpretations, are of interest within many areas of theoretical physics. The results of our model for all calculations show that the ground state binding energy of Lithium nucleus with these potentials are very close to the ones obtained in experiments.

  3. 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...

  4. Structure of the nucleotide-binding subunit B of the energy producer A1A0 ATP synthase in complex with adenosine diphosphate.

    Science.gov (United States)

    Kumar, Anil; Manimekalai, Malathy Sony Subramanian; Grüber, Gerhard

    2008-11-01

    A1A0 ATP synthases are the major energy producers in archaea. Like the related prokaryotic and eukaryotic F1F0 ATP synthases, they are responsible for most of the synthesis of adenosine triphosphate. The catalytic events of A1A0 ATP synthases take place inside the A3B3 hexamer of the A1 domain. Recently, the crystallographic structure of the nucleotide-free subunit B of Methanosarcina mazei Gö1 A1A0 ATP synthase has been determined at 1.5 A resolution. To understand more about the nucleotide-binding mechanism, a protocol has been developed to crystallize the subunit B-ADP complex. The crystallographic structure of this complex has been solved at 2.7 A resolution. The ADP occupies a position between the essential phosphate-binding loop and amino-acid residue Phe149, which are involved in the binding of the antibiotic efrapeptin in the related F1F0 ATP synthases. This trapped ADP location is about 13 A distant from its final binding site and is therefore called the transition ADP-binding position. In the trapped ADP position the structure of subunit B adopts a different conformation, mainly in its C-terminal domain and also in the final nucleotide-binding site of the central alphabeta-domain. This atomic model provides insight into how the substrate enters into the nucleotide-binding protein and thereby into the catalytic A3B3 domain. PMID:19020348

  5. Binding Energies and Scattering Observables in the 4^He_3 Atomic System

    OpenAIRE

    Motovilov, A. K.; Sandhas, W.; Sofianos, S. A.; Kolganova, E. A.

    1999-01-01

    The ^4He_3 bound states and the scattering of a ^4He atom off a ^4He dimer at ultra-low energies are investigated using a hard-core version of the Faddeev differential equations. Various realistic ^4He-^4He interactions were employed, amomg them the LM2M2 potential by Aziz and Slaman and the recent TTY potential by Tang, Toennies and Yiu. The ground state and the excited (Efimov) state obtained are compared with other results. The scattering lengths and the atom-diatom phase shifts were calcu...

  6. Binding energy and optical properties of an off-center hydrogenic donor impurity in a spherical quantum dot placed at the center of a cylindrical nano-wire

    International Nuclear Information System (INIS)

    The binding energy as well as the linear, third-order nonlinear and total optical absorption coefficient and refractive index changes of an off-center hydrogenic donor impurity in an InAs spherical quantum dot placed at the center of a GaAs cylindrical nano-wire have been investigated. In this regard, the effective-mass approximation approach is considered and eigenvalues and corresponding eigenfunctions are calculated via the finite element method. The binding energy is plotted as a function of the dot size and impurity position along with optical properties as a function of photon energy. In this study two different directions have been considered for impurity position, along the nano-wire axis and perpendicular to it. It has been found that the binding energy, absorption coefficient and refractive index changes are impressively affected not only by the dot radius but also by the position of the impurity and its direction. Additionally, the optical saturation can be tuned by the direction of the impurity and incident optical intensity. -- Highlights: • We consider spherical quantum dot located at the center of a cylindrical nano-wire. • An off-center hydrogenic donor impurity is considered in the system. • Binding energy is affected by orientation of impurity and its distance from center. • Saturation depends on the orientation of impurity position. • By shifting impurity position, orientation and dot radius blue- and red-shifts appear

  7. New measurements of the sticking coefficient and binding energy of molecules on non-porous amorphous solid water in the submonolayer regime

    Science.gov (United States)

    He, Jiao; Acharyya, Kinsuk; Emtiaz, S. M.; Vidali, Gianfranco

    2016-06-01

    Sticking and adsorption of molecules on dust grains are two important processes in gas-grain interactions. We accurately measured both the sticking coefficient and the binding energy of several key molecules on the surface of amorphous solid water as a function of coverage.A time-resolved scattering technique was used to measure sticking coefficient of H2, D2, N2, O2, CO, CH4, and CO2 on non-porous amorphous solid water (np-ASW) in the low coverage limit over a wide range of surface temperatures. We found that the time-resolved scattering technique is advantageous over the conventional King-Wells method that underestimates the sticking coefficient. Based on the measured values we suggest a useful general formula of the sticking coefficient as a function of grain temperature and molecule-surface binding energy.We measured the binding energy of N2, CO, O2, CH4, and CO2 on np-ASW, and of N2 and CO on porous amorphous solid water (p-ASW). 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 CO2 forms clusters on np-ASW surface even at very low coverage; this may help in explaining the segregation of CO2 in ices. The binding energies of N2, CO, O2, and CH4 on np-ASW decrease with coverage in the submonolayer regime. Their values in 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 dense clouds 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 ices stays much longer and to higher temperature on the grain surface compared to the case using single value energies as currently done in astrochemical models.This work was supported in

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Hydrogenic impurity binding energy in vertically coupled Ga{sub 1-x}Al{sub x}As quantum-dots under hydrostatic pressure and applied electric field

    Energy Technology Data Exchange (ETDEWEB)

    Duque, C.M. [Instituto de Fisica, Universidad de Antioquia, AA 1226, Medellin (Colombia); Barseghyan, M.G. [Department of Solid State Physics, Yerevan State University, Al. Manookian 1, 0025 Yerevan (Armenia); Duque, C.A., E-mail: cduque@fisica.udea.edu.c [Instituto de Fisica, Universidad de Antioquia, AA 1226, Medellin (Colombia)

    2009-12-15

    This work deals with a theoretical study, using a variational method and the effective mass approximation, of the ground state binding energy of a hydrogenic donor impurity in a vertically coupled multiple quantum dot structure under the effects of hydrostatic pressure and in-growth direction applied electric field. The low dimensional structure consists of three cylindrical shaped GaAs quantum dots coupled by Ga{sub 1-x}Al{sub x}As barriers. For the hydrostatic pressure has been considered the GAMMA-X crossover in the Ga{sub 1-x}Al{sub x}As material. As a general, the results show that: (1) the binding energy as a function of the impurity position has a similar shape to that shown by the electron wave function without the Coulomb interaction, (2) the presence of the electric field changes dramatically the binding energy profile destroying (favoring) the symmetry in the structures, and (3) depending on the impurity position the binding energy can increase or decrease with the hydrostatic pressure mainly due to increases or decreases of the carrier-wave function symmetry by changing the height of the potential barrier.

  15. Relativistic correlation correction to the binding energies of the ground configuration of Beryllium-like, Neon-like, Magnesium-like and Argon-like ions

    CERN Document Server

    Santos, J P; Marques, J P; Parente, F; Desclaux, J P; Indelicato, P J; Rodriges, Gustavo C.; Marques, Jos\\'{e} P.; Desclaux, Jean-Paul; Indelicato, Paul

    2005-01-01

    Total electronic correlation correction to the binding energies of the isoelectronic series of Beryllium, Neon, Magnesium and Argon, are calculated in the framework of relativistic multiconfiguration Dirac-Fock method. Convergence of the correlation energies is studied as the active set of orbitals is increased. The Breit interaction is treated fully self-consistently. The final results can be used in the accurately determination of atomic masses from highly charged ions data obtained in Penning-trap experiments.

  16. Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

    OpenAIRE

    Fernandez Pacios, Luis; Gomez Casado, Cristina; Tordesillas Villuendas, Leticia; Palacín Gómez, Aranzazu; Sanchez-Monge Laguna De Rins, Maria Rosa; Díaz Perales, Araceli

    2012-01-01

    Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a co...

  17. Structure and Binding Energy of Double-Stranded A-DNA Mini-helices: Quantum-Chemical Study.

    Science.gov (United States)

    Zubatiuk, Tetiana; Kukuev, Maxim A; Korolyova, Alexandra S; Gorb, Leonid; Nyporko, Alexey; Hovorun, Dmytro; Leszczynski, Jerzy

    2015-10-01

    A-DNA is thought to play a significant biological role in gene expression due to its specific conformation and binding features. In this study, double-stranded mini-helices (dA:dT)3 and (dG:dC)3 in A-like DNA conformation were investigated. M06-2X/6-31G(d,p) method has been utilized to identify the optimal geometries and predict physicochemical parameters of these systems. The results show the ability of the corresponding mini-helices to preserve their A-like conformation under the influences of solvent, charge, and Na(+) counterions. Presented structural and energetic data offer evidence that two steps of GG/CC or AA/TT are already enough to turn the DNA helix to generate different forms by favoring specific values of roll and slide at a local level. Our calculations support the experimentally known fact that AA/TT steps prefer the B-form over the A-ones, whereas GG/CC steps may be found in either the B- or A-form. The stability of mini-helices at the level of total energy analysis, ΔEtotal((A–B)), is discussed. PMID:26356008

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

    International Nuclear Information System (INIS)

    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

  19. 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.

  20. Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA.

    Science.gov (United States)

    Carra, Claudio; Cucinotta, Francis A

    2012-06-01

    The eukaryotic replication protein A (RPA) has several pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Moreover, RPA seems to have a crucial role in organizing the sequential assembly of DNA processing proteins along single stranded DNA (ssDNA). The strong RPA affinity for ssDNA, K(A) between 10(-9)-10(-10) M, is characterized by a low cooperativity with minor variation for changes on the nucleotide sequence. Recently, new data on RPA interactions was reported, including the binding free energy of the complex RPA70AB with dC(8) and dC(5), which has been estimated to be -10 ± 0.4 kcal mol(-1) and -7 ± 1 kcal mol(-1), respectively. In view of these results we performed a study based on molecular dynamics aimed to reproduce the absolute binding free energy of RPA70AB with the dC(5) and dC(8) oligonucleotides. We used several tools to analyze the binding free energy, rigidity, and time evolution of the complex. The results obtained by MM-PBSA method, with the use of ligand free geometry as a reference for the receptor in the separate trajectory approach, are in excellent agreement with the experimental data, with ±4 kcal mol(-1) error. This result shows that the MM-PB(GB)SA methods can provide accurate quantitative estimates of the binding free energy for interacting complexes when appropriate geometries are used for the receptor, ligand and complex. The decomposition of the MM-GBSA energy for each residue in the receptor allowed us to correlate the change of the affinity of the mutated protein with the ΔG(gas+sol) contribution of the residue considered in the mutation. The agreement with experiment is optimal and a strong change in the binding free energy can be considered as the dominant factor in the loss for the binding affinity resulting from mutation. PMID:22116609

  1. 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. PMID:27488185

  2. 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.

  3. Effect of medium dependent binding energies on inferring the temperatures and freeze-out density of disassembling hot nuclear matter from cluster yields

    CERN Document Server

    Shlomo, S; Natowitz, J B; Qin, L; Hagel, K; Wada, R; Bonasera, A

    2009-01-01

    We explore the abundance of light clusters in asymmetric nuclear matter at subsaturation density. With increasing density, binding energies and wave functions are modified due to medium effects. The method of Albergo, Costa, Costanzo and Rubbino (ACCR) for determining the temperature and free nucleon density of a disassembling hot nuclear source from fragment yields is modified to include, in addition to Coulomb effects and flow, also effects of medium modifications of cluster properties, which become of importance when the nuclear matter density is above 10$^{-3}$ fm$^{-3}$. We show how the analysis of cluster yields, to infer temperature and nucleon densities, is modified if the shifts in binding energies of in medium clusters are included. While, at low densities, the temperature calculated from given yields changes only modestly if medium effects are taken into account, larger discrepancies are observed when the nucleon densities are determined from measured yields.

  4. Effects of hydrostatic pressure on the donor binding energy and intra donor transition matrix elements in GaAs-GaAlAs quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Panahi, H. [Institutes for Studies in Theoretical Physics and Mathematics, Tehran 19395-1795 (Iran); Maleki, M. [Department of Physics, University of Guilan, Rasht 41335-1914 (Iran)

    2008-05-15

    The effects of hydrostatic pressure on the donor binding energy in GaAs-Ga{sub 0.7}Al{sub 0.3}As quantum wells have been studied in the effective mass approximation, using a variational approach for hydrogenic ground state 1s and excited states 2s, 2p{sub x}, 3p{sub x}. Results obtained show that the donor binding energy variation with the well width and the position of impurity under pressure is similar to that without pressure. The intra donor squared transition matrix elements are calculated as functions of impurity position in the presence of hydrostatic pressure. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  5. Observation of core-level binding energy shifts between (100) surface and bulk atoms of epitaxial CuInSe2

    International Nuclear Information System (INIS)

    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 CuInSe2, 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

  6. 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.

  7. How Similar Are Protein Folding and Protein Binding Nuclei? Examination of Vibrational Motions of Energy Hot Spots and Conserved Residues

    OpenAIRE

    Haliloglu, Turkan; Keskin, Ozlem; Ma, Buyong; Nussinov, Ruth

    2004-01-01

    The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and experimental hot spots at intermolecular binding interfaces overlap residues that vibrate with high frequencies. Similarly, conserved residues and hot spots are found in protein cores and are also observed to vibrate with high frequencies. In both cases, these residues contribute significantly to t...

  8. THEORETICAL-ANALYSIS OF THE O(1S) BINDING-ENERGY SHIFTS IN ALKALINE-EARTH OXIDES - CHEMICAL OR ELECTROSTATIC CONTRIBUTIONS

    NARCIS (Netherlands)

    PACCHIONI, G; BAGUS, PS

    1994-01-01

    We report results from ab initio cluster-model calculations on the O(1s) binding energy (BE) in the alkaline-earth oxides, MgO, CaO, SrO, and BaO; all these oxides have a cubic lattice structure. We have obtained values for both the initial- and final-state BE's. A simple point-charge model, where a

  9. First-Principle Framework for Total Charging Energies in Electrocatalytic Materials and Charge-Responsive Molecular Binding at Gas-Surface Interfaces.

    Science.gov (United States)

    Tan, Xin; Tahini, Hassan A; Seal, Prasenjit; Smith, Sean C

    2016-05-01

    Heterogeneous charge-responsive molecular binding to electrocatalytic materials has been predicted in several recent works. This phenomenon offers the possibility of using voltage to manipulate the strength of the binding interaction with the target gas molecule and thereby circumvent thermochemistry constraints, which inhibit achieving both efficient binding and facile release of important targets such as CO2 and H2. Stability analysis of such charge-induced molecular adsorption has been beyond the reach of existing first-principle approaches. Here, we draw on concepts from semiconductor physics and density functional theory to develop a first principle theoretical approach that allows calculation of the change in total energy of the supercell due to charging. Coupled with the calculated adsorption energy of gas molecules at any given charge, this allows a complete description of the energetics of the charge-induced molecular adsorption process. Using CO2 molecular adsorption onto negatively charged h-BN (wide-gap semiconductor) and g-C4N3 (half metal) as example cases, our analysis reveals that - while adsorption is exothermic after charge is introduced - the overall adsorption processes are not intrinsically spontaneous due to the energetic cost of charging the materials. The energies needed to overcome the barriers of these processes are 2.10 and 0.43 eV for h-BN and g-C4N3, respectively. This first principle approach opens up new pathways for a more complete description of charge-induced and electrocatalytic processes. PMID:27067063

  10. 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

  11. 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.

  12. 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)

    Huang, Yu-ming M.; Kizhake, Smitha; Natarajan, Amarnath; Chang, Chia-en A.

    2016-01-01

    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. PMID

  13. Relativistic correlation correction to the binding energies of the ground configuration of beryllium-like, neon-like, magnesium-like and argon-like ions

    International Nuclear Information System (INIS)

    Total electronic correlation corrections to the binding energies of the isoelectronic series of beryllium, neon, magnesium and argon, are calculated in the framework of relativistic multiconfiguration Dirac-Fock method. Convergence of the correlation energies is studied as the active set of orbitals is increased. The Breit interaction is treated fully self-consistently. We have shown that accurate results can be achieved if excitations to all shells up to the n = 6 shell are included. The final results can be used in the accurately determination of atomic masses from highly charged ions data obtained in Penning-trap experiments

  14. 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.

  15. Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies

    Directory of Open Access Journals (Sweden)

    Stegmaier Philip

    2010-05-01

    Full Text Available Abstract Background Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription factors in the literature, however, for many of them the corresponding DNA-binding motifs remain uncharacterized. Results The position weight matrices (PWMs of transcription factors from different structural classes have been determined using a knowledge-based statistical potential. The scoring function calibrated against crystallographic data on protein-DNA contacts recovered PWMs of various members of widely studied transcription factor families such as p53 and NF-κB. Where it was possible, extensive comparison to experimental binding affinity data and other physical models was made. Although the p50p50, p50RelB, and p50p65 dimers belong to the same family, particular differences in their PWMs were detected, thereby suggesting possibly different in vivo binding modes. The PWMs of p63 and p73 were computed on the basis of homology modeling and their performance was studied using upstream sequences of 85 p53/p73-regulated human genes. Interestingly, about half of the p63 and p73 hits reported by the Match algorithm in the altogether 126 promoters lay more than 2 kb upstream of the corresponding transcription start sites, which deviates from the common assumption that most regulatory sites are located more proximal to the TSS. The fact that in most of the cases the binding sites of p63 and p73 did not overlap with the p53 sites suggests that p63 and p73 could influence the p53 transcriptional activity cooperatively. The newly computed p50p50 PWM recovered 5 more experimental binding sites than the corresponding TRANSFAC matrix, while both PWMs showed comparable receiver operator characteristics. Conclusions A novel algorithm was developed to calculate position weight matrices from protein-DNA complex structures. The proposed algorithm was extensively validated

  16. Quarkonium Binding and Entropic Force

    CERN Document Server

    Satz, Helmut

    2015-01-01

    A Q-Qbar bound state represents a balance between repulsive kinetic and attractive potential energy. In a hot quark-gluon plasma, the interaction potential experiences medium effects. Color screening modifies the attractive binding force between the quarks, while the increase of entropy with Q-Qbar separation gives rise to a growing repulsion. We study the role of these phenomena for in-medium Q-Qbar binding and dissociation. It is found that the relevant potential for Q-Qbar binding is the free energy F; with increasing Q-Qbar separation, further binding through the internal energy U is compensated by repulsive entropic effects.

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

    Energy Technology Data Exchange (ETDEWEB)

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2015-03-07

    We report the variation of the binding energy of the formic acid dimer at the CCSD(T)/ Complete Basis Set limit and examine the validity of the BSSE-correction, previously challenged by Kalescky, Kraka and Cremer [J. Chem. Phys. 140 (2014) 084315]. Our best estimate of D0=14.3±0.1 kcal/mol is in excellent agreement with the experimental value of 14.22±0.12 kcal/mol. The BSSE correction is indeed valid for this system since it exhibits the expected behavior of decreasing with increasing basis set size and its inclusion produces the same limit (within 0.1 kcal/mol) as the one obtained from extrapolation of the uncorrected binding energy. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. A portion of this research was performed using the Molecular Science Computing Facility (MSCF) in EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at PNNL.

  18. Proton-bound dimers of nitrogen heterocyclic molecules: Substituent effects on the structures and binding energies of homodimers of diazine, triazine, and fluoropyridine

    Energy Technology Data Exchange (ETDEWEB)

    Attah, Isaac K.; Platt, Sean P.; Meot-Ner, Michael; El-Shall, M. S., E-mail: mselshal@vcu.edu [Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006 (United States); Aziz, Saadullah G.; Alyoubi, Abdulrahman O. [Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia)

    2014-03-21

    The bonding energies of proton-bound homodimers BH{sup +}B were measured by ion mobility equilibrium studies and calculated at the DFT B3LYP/6-311++G{sup **} level, for a series of nitrogen heterocyclic molecules (B) with electron-withdrawing in-ring N and on-ring F substituents. The binding energies (ΔH°{sub dissoc}) of the proton-bound dimers (BH{sup +}B) vary significantly, from 29.7 to 18.1 kcal/mol, decreasing linearly with decreasing the proton affinity of the monomer (B). This trend differs significantly from the constant binding energies of most homodimers of other organic nitrogen and oxygen bases. The experimentally measured ΔH°{sub dissoc} for (1,3-diazine){sub 2}H{sup +}, i.e., (pyrimidine){sub 2}H{sup +} and (3-F-pyridine){sub 2}H{sup +} are 22.7 and 23.0 kcal/mol, respectively. The measured ΔH°{sub dissoc} for the pyrimidine{sup ·+}(3-F-pyridine) radical cation dimer (19.2 kcal/mol) is signifcantly lower than that of the proton-bound homodimers of pyrimidine and 3-F-pyridine, reflecting the stronger interaction in the ionic H-bond of the protonated dimers. The calculated binding energies for (1,2-diazine){sub 2}H{sup +}, (pyridine){sub 2}H{sup +}, (2-F-pyridine){sub 2}H{sup +}, (3-F-pyridine){sub 2}H{sup +}, (2,6-di-F-pyridine){sub 2}H{sup +}, (4-F-pyridine){sub 2}H{sup +}, (1,3-diazine){sub 2}H{sup +}, (1,4-diazine){sub 2}H{sup +}, (1,3,5-triazine){sub 2}H{sup +}, and (pentafluoropyridine){sub 2}H{sup +} are 29.7, 24.9, 24.8, 23.3, 23.2, 23.0, 22.4, 21.9, 19.3, and 18.1 kcal/mol, respectively. The electron-withdrawing substituents form internal dipoles whose electrostatic interactions contribute to both the decreased proton affinities of (B) and the decreased binding energies of the protonated dimers BH{sup +}B. The bonding energies also vary with rotation about the hydrogen bond, and they decrease in rotamers where the internal dipoles of the components are aligned efficiently for inter-ring repulsion. For compounds substituted at the 3 or 4

  19. Proton-bound dimers of nitrogen heterocyclic molecules: Substituent effects on the structures and binding energies of homodimers of diazine, triazine, and fluoropyridine

    International Nuclear Information System (INIS)

    The bonding energies of proton-bound homodimers BH+B were measured by ion mobility equilibrium studies and calculated at the DFT B3LYP/6-311++G** level, for a series of nitrogen heterocyclic molecules (B) with electron-withdrawing in-ring N and on-ring F substituents. The binding energies (ΔH°dissoc) of the proton-bound dimers (BH+B) vary significantly, from 29.7 to 18.1 kcal/mol, decreasing linearly with decreasing the proton affinity of the monomer (B). This trend differs significantly from the constant binding energies of most homodimers of other organic nitrogen and oxygen bases. The experimentally measured ΔH°dissoc for (1,3-diazine)2H+, i.e., (pyrimidine)2H+ and (3-F-pyridine)2H+ are 22.7 and 23.0 kcal/mol, respectively. The measured ΔH°dissoc for the pyrimidine·+(3-F-pyridine) radical cation dimer (19.2 kcal/mol) is signifcantly lower than that of the proton-bound homodimers of pyrimidine and 3-F-pyridine, reflecting the stronger interaction in the ionic H-bond of the protonated dimers. The calculated binding energies for (1,2-diazine)2H+, (pyridine)2H+, (2-F-pyridine)2H+, (3-F-pyridine)2H+, (2,6-di-F-pyridine)2H+, (4-F-pyridine)2H+, (1,3-diazine)2H+, (1,4-diazine)2H+, (1,3,5-triazine)2H+, and (pentafluoropyridine)2H+ are 29.7, 24.9, 24.8, 23.3, 23.2, 23.0, 22.4, 21.9, 19.3, and 18.1 kcal/mol, respectively. The electron-withdrawing substituents form internal dipoles whose electrostatic interactions contribute to both the decreased proton affinities of (B) and the decreased binding energies of the protonated dimers BH+B. The bonding energies also vary with rotation about the hydrogen bond, and they decrease in rotamers where the internal dipoles of the components are aligned efficiently for inter-ring repulsion. For compounds substituted at the 3 or 4 (meta or para) positions, the lowest energy rotamers are T-shaped with the planes of the two rings rotated by 90° about the hydrogen bond, while the planar rotamers are weakened by repulsion between the

  20. 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.

  1. Binding Energies from Diffusion Monte Carlo for the MB-pol H_2O and D_2O Dimer: A Comparison to Experimental Values

    CERN Document Server

    Mallory, Joel

    2015-01-01

    The Diffusion Monte Carlo (DMC) method is applied to compute the ground state energies of the water monomer and dimer and their D 2 O isotopomers using MB-pol; the most recent and most accurate ab inito- based potential energy surface (PES). MB-pol has already demonstrated excellent agreement with high level electronic structure data, as well as agreement with some experimental, spectroscopic, and thermodynamic data. Here, the DMC binding energies of (H 2 O) 2 and (D 2 O) 2 agree with the corresponding values obtained from velocity map imaging within, respectively, 0.01 and 0.02 kcal/mol. This work adds two more valuable data points that highlight the accuracy of the MB-pol PES.

  2. Binding energies from diffusion Monte Carlo for the MB-pol H{sub 2}O and D{sub 2}O dimer: A comparison to experimental values

    Energy Technology Data Exchange (ETDEWEB)

    Mallory, Joel D.; Mandelshtam, Vladimir A. [Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697 (United States)

    2015-10-14

    The diffusion Monte Carlo (DMC) method is applied to compute the ground state energies of the water monomer and dimer and their D{sub 2}O isotopomers using MB-pol; the most recent and most accurate ab inito-based potential energy surface (PES). MB-pol has already demonstrated excellent agreement with high level electronic structure data, as well as agreement with some experimental, spectroscopic, and thermodynamic data. Here, the DMC binding energies of (H{sub 2}O){sub 2} and (D{sub 2}O){sub 2} agree with the corresponding values obtained from velocity map imaging within, respectively, 0.01 and 0.02 kcal/mol. This work adds two more valuable data points that highlight the accuracy of the MB-pol PES.

  3. 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.

  4. 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.

  5. Estimating effective higher order terms in the post-Newtonian binding energy and gravitational-wave flux: Non-spinning compact binary inspiral

    CERN Document Server

    Kapadia, Shasvath J; Ajith, Parameswaran

    2016-01-01

    In the adiabatic post-Newtonian (PN) approximation, the phase evolution of gravitational waves (GWs) from inspiralling compact binaries in quasicircular orbits is computed by equating the change in binding energy with the GW flux. This energy balance equation can be solved in different ways, which result in multiple approximants of the PN waveforms. Due to the poor convergence of the PN expansion, these approximants tend to differ from each other during the late inspiral. Which of these approximants should be chosen as templates for detection and parameter estimation of GWs from inspiraling compact binaries is not obvious. In this paper, we present estimates of the effective higher order (beyond the currently available 4PN and 3.5PN) non-spinning terms in the PN expansion of the binding energy and the GW flux that minimize the difference of multiple PN approximants (TaylorT1, TaylorT2, TaylorT4, TaylorF2) with effective one body waveforms calibrated to numerical relativity (EOBNR). We show that PN approximant...

  6. Scalar and Spinor Particles with Low Binding Energy in the Strong Stationary Magnetic Field Studied by Means of Two-and Three-Dimensional Models

    CERN Document Server

    Rodionov, V N

    2007-01-01

    On the basis of analytic solutions of Schrodinger and Pauli equations for a uniform magnetic field and a single attractive $\\delta({\\bf r})$-potential the equations for the bound one-active electron states are discussed. It is vary important that ground electron states in the magnetic field essentially different from the analog state of spin-0 particles that binding energy has been intensively studied at more then forty years ago. We show that binding energy equations for spin-1/2 particles can be obtained without using of a well-known language of boundary conditions in the model of $\\delta$-potential that has been developed in pioneering works. Obtained equations are used for the analytically calculation of the energy level displacements, which demonstrate nonlinear dependencies on field intensities. It is shown that in a case of the weak intensity a magnetic field indeed plays a stabilizing role in considering systems. However the strong magnetic field shows the opposite action. We are expected that these p...

  7. 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.

  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. PMID:27421423

  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

    Energy Technology Data Exchange (ETDEWEB)

    Miliordos, Evangelos; Xantheas, Sotiris S., E-mail: sotiris.xantheas@pnnl.gov [Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352 (United States)

    2015-03-07

    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 D{sub e} = − 16.1 ± 0.1 kcal/mol and for D{sub 0} = − 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of −14.22 ± 0.12 kcal/mol.

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

    OpenAIRE

    Marharyta Petukh; Minghui Li; Emil Alexov

    2015-01-01

    Author Summary Developing methods for accurate prediction of effects of amino acid substitutions on protein-protein affinity is important for both understanding disease-causing mechanism of missense mutations and guiding protein engineering. For both purposes, there is a need for accurate methods primarily based on first principle calculations, while being fast enough to handle large number of cases. Here we report a new method, the Single Amino Acid Mutation based change in Binding free Ener...

  11. 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.

  12. 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.

  13. Role of hydrophobic mutations on the binding affinity and stability of blood coagulation factor VIIIa: a computational molecular dynamics and free-energy analysis.

    Science.gov (United States)

    Venkateswarlu, Divi

    2014-07-18

    Factor VIIIa is a non-covalently bound hetero-trimer among A1, A2 and A3-C1-C2 domains and an essential co-factor for factor IXa enzyme during proteolytic activation of factor X zymogen. The relatively weak interactions between A2 and the interface A1/A3 domains dampen the functional stability of FVIIIa in plasma and results in rapid degradation. We studied the mutational effect of three charged residues (Asp519, Glu665 and Asp666) to several hydrophobic residues by molecular dynamics simulations. Analysis of the binding free energy by MM-PBSA and MM-GBSA methods shows that the mutation of Asp519 and Glu665 residues to either Val or Ala enhance the A2 domain binding affinity in agreement with the experimental site-specific mutagenesis data. Mutation of Asp666 to Val, Tyr, Met and Phe showed largest improvement in the A2-domain binding among the eight hydrophobic mutants studied. Our studies suggest that the enrichment of hydrophobic interactions in the buried surface regions of A2 domain plays crucial role in improving the overall stability of FVIIIa. PMID:24952158

  14. Involvement of the Acyl-CoA binding domain containing 7 in the control of food intake and energy expenditure in mice.

    Science.gov (United States)

    Lanfray, Damien; Caron, Alexandre; Roy, Marie-Claude; Laplante, Mathieu; Morin, Fabrice; Leprince, Jérôme; Tonon, Marie-Christine; Richard, Denis

    2016-01-01

    Acyl-CoA binding domain-containing 7 (Acbd7) is a paralog gene of the diazepam-binding inhibitor/Acyl-CoA binding protein in which single nucleotide polymorphism has recently been associated with obesity in humans. In this report, we provide converging evidence indicating that a splice variant isoform of the Acbd7 mRNA is expressed and translated by some POMC and GABAergic-neurons in the hypothalamic arcuate nucleus (ARC). We have demonstrated that the ARC ACBD7 isoform was produced and processed into a bioactive peptide referred to as nonadecaneuropeptide (NDN) in response to catabolic signals. We have characterized NDN as a potent anorexigenic signal acting through an uncharacterized endozepine G protein-coupled receptor and subsequently via the melanocortin system. Our results suggest that ACBD7-producing neurons participate in the hypothalamic leptin signalling pathway. Taken together, these data suggest that ACBD7-producing neurons are involved in the hypothalamic control exerted on food intake and energy expenditure by the leptin-melanocortin pathway. PMID:26880548

  15. Exploring the mechanism of how tvMyb2 recognizes and binds ap65-1 by molecular dynamics simulations and free energy calculations.

    Science.gov (United States)

    Li, Wei-Kang; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-01-01

    TvMyb2, one of the Myb-like transcriptional factors in Trichomonas vaginalis, binds to two closely spaced promoter sites, MRE-1/MRE-2r and MRE-2f, on the ap65-1 gene. However, detailed dynamical structural characteristics of the tvMyb2-ap65-1 complex and a detailed study of the protein in the complex have not been done. Focused on a specific tvMyb2-MRE-2-13 complex (PDB code: ) and a series of mutants K51A, R84A and R87A, we applied molecular dynamics (MD) simulation and molecular mechanics generalized Born surface area (MM-GBSA) free energy calculations to examine the role of the tvMyb2 protein in recognition interaction. The simulation results indicate that tvMyb2 becomes stable when it binds the DNA duplex. A series of mutants, K51A, R84A and R87A, have been followed, and the results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on recognition and binding to ap65-1 DNA. Our work gives important information to understand the interactions of tvMyb2 with ap65-1. PMID:26548411

  16. 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

  17. 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

  18. ATP–Binding Cassette Transporter Structure Changes Detected by Intramolecular Fluorescence Energy Transfer for High-Throughput Screening

    OpenAIRE

    Iram, Surtaj H.; Gruber, Simon J.; Raguimova, Olga N.; Thomas, David D.; Seth L Robia

    2015-01-01

    Multidrug resistance protein 1 (MRP1) actively transports a wide variety of drugs out of cells. To quantify MRP1 structural dynamics, we engineered a “two-color MRP1” construct by fusing green fluorescent protein (GFP) and TagRFP to MRP1 nucleotide–binding domains NBD1 and NBD2, respectively. The recombinant MRP1 protein expressed and trafficked normally to the plasma membrane. Two-color MRP1 transport activity was normal, as shown by vesicular transport of [3H]17β-estradiol-17-β-(d-glucuroni...

  19. 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...

  20. 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.

  1. Photoelectron spectroscopy of aqueous solutions: Streaming potentials of NaX (X = Cl, Br, and I) solutions and electron binding energies of liquid water and X−

    International Nuclear Information System (INIS)

    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

  2. Dual inhibitors for aspartic proteases HIV-1 PR and renin: advancements in AIDS-hypertension-diabetes linkage via molecular dynamics, inhibition assays, and binding free energy calculations.

    Science.gov (United States)

    Tzoupis, Haralambos; Leonis, Georgios; Megariotis, Grigorios; Supuran, Claudiu T; Mavromoustakos, Thomas; Papadopoulos, Manthos G

    2012-06-28

    Human immunodeficiency virus type 1 protease (HIV-1 PR) and renin are primary targets toward AIDS and hypertension therapies, respectively. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free-energy calculations and inhibition assays for canagliflozin, an antidiabetic agent verified its effective binding to both proteins (ΔG(pred) = -9.1 kcal mol(-1) for canagliflozin-renin; K(i,exp)= 628 nM for canagliflozin-HIV-1 PR). Moreover, drugs aliskiren (a renin inhibitor) and darunavir (an HIV-1 PR inhibitor) showed high affinity for HIV-1 PR (K(i,exp)= 76.5 nM) and renin (K(i,pred)= 261 nM), respectively. Importantly, a high correlation was observed between experimental and predicted binding energies (r(2) = 0.92). This study suggests that canagliflozin, aliskiren, and darunavir may induce profound effects toward dual HIV-1 PR and renin inhibition. Since patients on highly active antiretroviral therapy (HAART) have a high risk of developing hypertension and diabetes, aliskiren-based or canagliflozin-based drug design against HIV-1 PR may eliminate these side-effects and also facilitate AIDS therapy. PMID:22621689

  3. Standard free energies of binding of solute to proteins in aqueous medium. Part 2. Analysis of data obtained from equilibrium dialysis and isopiestic experiments.

    Science.gov (United States)

    Chattoraj, D K; Biswas, S C; Mahapatra, P K; Chatterjee, S

    1999-03-01

    In an earlier publication by Chattoraj et al. [Biophysical Chemistry 63 (1996) 37], a generalized equation for standard free energy of (delta G0) interaction of surfactant, inorganic salts and aqueous solvent with protein, forming a single phase has been deduced on strict thermodynamic grounds. In the present paper, this equation has been utilized to calculate delta G0 in kilojoules per kilogram of different proteins for the change of bulk surfactant activity from zero to unity in the mole fraction scale. Values of binding interactions of CTAB, MTAB, DTAB and SDS to BSA, beta-lactoglobulin, gelatin, casein, myosin, lysozyme and their binary and ternary mixtures had already been determined in this laboratory at different surfactant concentrations, pH, ionic strength and temperature using an equilibrium dialysis technique. Values of delta G0 for saturated protein-surfactant complexes as well as unsaturated complexes are found to be equal. delta G0 is also found to vary linearly with maximum moles of surfactants bound to a kilogram of protein or protein mixture and the slope of this linear plot represents standard free energy delta G0B for the transfer of 1 mol of surfactant from the bulk for binding reaction with protein; -delta G0 values for different systems vary widely and the order of their magnitudes represents relative affinities of surfactants to proteins. Magnitude of -delta G0B on the other hand varies within a narrow range of 32-37 kJ/mol of surfactant. For interaction of SDS with BSA, close to the CMC, values of delta G0 are very high due to the formation of micelles of protein-bound surfactants. Values of delta G0 for negative binding of inorganic salts to proteins and protein mixtures have been evaluated using our generalized equation in which excess binding values of water and salts have been calculated from the data obtained from our previous isopiestic experiments. delta G0 values in these cases are positive due to the excess hydration of proteins

  4. Solute-vacancy binding in aluminum

    International Nuclear Information System (INIS)

    Previous efforts to understand solute-vacancy binding in aluminum alloys have been hampered by a scarcity of reliable, quantitative experimental measurements. Here, we report a large database of solute-vacancy binding energies determined from first-principles density functional calculations. The calculated binding energies agree well with accurate measurements where available, and provide an accurate predictor of solute-vacancy binding in other systems. We find: (i) some common solutes in commercial Al alloys (e.g., Cu and Mg) possess either very weak (Cu), or even repulsive (Mg), binding energies. Hence, we assert that some previously reported large binding energies for these solutes are erroneous. (ii) Large binding energies are found for Sn, Cd and In, confirming the proposed mechanism for the reduced natural aging in Al-Cu alloys containing microalloying additions of these solutes. (iii) In addition, we predict that similar reduction in natural aging should occur with additions of Si, Ge and Au. (iv) Even larger binding energies are found for other solutes (e.g., Pb, Bi, Sr, Ba), but these solutes possess essentially no solubility in Al. (v) We have explored the physical effects controlling solute-vacancy binding in Al. We find that there is a strong correlation between binding energy and solute size, with larger solute atoms possessing a stronger binding with vacancies. (vi) Most transition-metal 3d solutes do not bind strongly with vacancies, and some are even energetically strongly repelled from vacancies, particularly for the early 3d solutes, Ti and V

  5. Exploring the mechanism how AF9 recognizes and binds H3K9ac by molecular dynamics simulations and free energy calculations.

    Science.gov (United States)

    Wang, Quan; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-11-01

    Histone acetylation is a very important regulatory mechanism in gene expression in the chromatin context. A new protein family-YEATS domains have been found as a novel histone acetylation reader, which could specific recognize the histone lysine acetylation. AF9 is an important one in the YEATS family. Focused on the AF9-H3K9ac (K9 acetylation) complex (ALY) (PDB code: 4TMP) and a serials of mutants, MUT (the acetyllsine of H3K9ac was mutated to lysine), F59A, G77A, and D103A, we applied molecular dynamics simulation and molecular mechanics Poisson-Boltzmann (MM-PBSA) free energy calculations to examine the role of AF9 protein in recognition interaction. The simulation results and analysis indicate that some residues of the protein have significant influence on recognition and binding to H3K9ac peptides and hydrophobic surface show the hydrophobic interactions play an important role in the binding. Our work can give important information to understand how the protein AF9 recognizes the peptides H3K9ac. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 779-786, 2016. PMID:27312527

  6. 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.

  7. The impact of obesity, fat distribution, and energy restriction on insulin-like growth factor-1 (IGF-1), IGF-binding protein-3, insulin, and growth hormone

    DEFF Research Database (Denmark)

    Rasmussen, M H; Frystyk, Jan; Andersen, T;

    1994-01-01

    The aim of this study was to characterize the association between serum insulin-like growth factor-1 (IGF-1) and obesity, as well as fat distribution, before and during moderate energy restriction (1,200 kcal/d). In 51 females and nine males having a body mass index (BMI) between 27 and 39 kg/m2......, relationships between serum IGF-1, IGF-binding protein-3 (IGFBP-3), insulin, growth hormone (GH), blood glucose, and anthropometric measurements of body fat were examined. The patients were studied before treatment and again after 8 and 16 weeks of dieting. Visceral adipose tissue (AT) was estimated...... = .02) weeks of dietary treatment. Both serum IGF-1 and insulin levels were positively correlated with serum IGFBP-3 levels (r = .34, P = .009 and r = .34, P = .008, respectively). We conclude that IGF-1 levels in obese females reflect the intraabdominal fat mass rather than obesity per se. IGF-1...

  8. 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...

  9. Benchmark binding energies of ammonium and alkyl-ammonium ions interacting with water. Are ammonium-water hydrogen bonds strong?

    Science.gov (United States)

    Vallet, Valérie; Masella, Michel

    2015-01-01

    Alkyl-ammonium ion/water interactions are investigated using high level quantum computations, yielding thermodynamics data in good agreement with gas-phase experiments. Alkylation and hydration lead to weaken the NHsbnd O hydrogen bonds. Upon complete hydration by four water molecules, their main features are close to those of the OHsbnd O bond in the isolated water dimer. Energy decomposition analyses indicate that hydration of alkyl-ammonium ions are mainly due to electrostatic/polarization effects, as for hard monoatomic cations, but with a larger effect of dispersion.

  10. 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.

  11. 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...

  12. 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

  13. The effects of optical phonon on the binding energy of bound polaron in a wurtzite ZnO/Mg{sub x}Zn{sub 1–x}O quantum well

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Feng-Qi [College of Physics and Electronic Information, Inner Mongolia Normal University, Inner Mongolia Key Laboratory for Physics and Chemistry of Functional Materials, Hohhot 010022 (China); Guo, Zi-Zheng [Department of Applied Physics, College of Science, South China Agricultural University, Guangzhou 510642 (China); Zhu, Jun, E-mail: jiulye@126.com [School of Physical Science and Technology, Inner Mongolia University, Hohhot 010022 (China)

    2014-07-07

    An improved Lee-Low-Pines intermediate coupling method is used to study the energies and binding energies of bound polarons in a wurtzite ZnO/Mg{sub x}Zn{sub 1–x}O quantum well. The contributions from different branches of long-wave optical phonons, i.e., confined optical phonons, interface optical phonons, and half-space optical phonons are considered. In addition to electron-phonon interaction, the impurity-phonon interaction, and the anisotropy of material parameters, such as phonon frequency, electron effective mass, and dielectric constant, are also included in our computation. Ground-state energies, binding energies and detailed phonon contributions from various phonons as functions of well width, impurity position and composition are presented. Our result suggests that total phonon contribution to ground state and binding energies in the studied wurtzite ZnO/Mg₀.₃Zn₀.₇O quantum wells varies between 28–23 meV and 62–45 meV, respectively, which are much larger than the corresponding values (about 3.2–1.8 meV and 1.6–0.3 meV) in GaAs/Al₀.₃Ga₀.₇As quantum wells. For a narrower quantum well, the phonon contribution mainly comes from interface and half-space phonons, for a wider quantum well, most of phonon contribution originates from confined phonons. The contribution from all the phonon modes to binding energies increases slowly either when impurity moves far away from the well center in the z direction or with the increase in magnesium composition (x). It is found that different phonons have different influences on the binding energies of bound polarons. Furthermore, the phonon contributions to binding energies as functions of well width, impurity position, and composition are very different from one another. In general, the electron-optical phonon interaction and the impurity center-optical phonon interaction play an important role in electronic states of ZnO-based quantum wells and cannot be neglected.

  14. 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.

  15. Breaking the bottleneck: Use of molecular tailoring approach for the estimation of binding energies at MP2/CBS limit for large water clusters

    Science.gov (United States)

    Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R.

    2016-03-01

    A pragmatic method based on the molecular tailoring approach (MTA) for estimating the complete basis set (CBS) limit at Møller-Plesset second order perturbation (MP2) theory accurately for large molecular clusters with limited computational resources is developed. It is applied to water clusters, (H2O)n (n = 7, 8, 10, 16, 17, and 25) optimized employing aug-cc-pVDZ (aVDZ) basis-set. Binding energies (BEs) of these clusters are estimated at the MP2/aug-cc-pVNZ (aVNZ) [N = T, Q, and 5 (whenever possible)] levels of theory employing grafted MTA (GMTA) methodology and are found to lie within 0.2 kcal/mol of the corresponding full calculation MP2 BE, wherever available. The results are extrapolated to CBS limit using a three point formula. The GMTA-MP2 calculations are feasible on off-the-shelf hardware and show around 50%-65% saving of computational time. The methodology has a potential for application to molecular clusters containing ˜100 atoms.

  16. Investigating the Weak to Evaluate the Strong: An Experimental Determination of the Electron Binding Energy of Carborane Anions and the Gas phase Acidity of Carborane Acids

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, Matthew M; Wang, Xue B; Reed, Christopher A; Wang, Lai S; Kass, Steven R

    2009-12-23

    Five CHB11X6Y5- carborane anions from the series X = Br, Cl, I and Y = H, Cl, CH3 were generated by electrospray ionization, and their reactivity with a series of Brønsted acids and electron transfer reagents were examined in the gas phase. The undecachlorocarborane acid, H(CHB11Cl11), was found to be far more acidic than the former record holder, (1-C4F9SO2)2NH (i.e., ΔH°acid = 241 ± 29 vs 291.1 ± 2.2 kcal mol-1) and bridges the gas-phase acidity and basicity scales for the first time. Its conjugate base, CHB11Cl11-, was found by photoelectron spectroscopy to have a remarkably large electron binding energy (6.35 ± 0.02 eV) but the value for the (1-C4F9SO2)2N- anion is even larger (6.5 ± 0.1 eV). Consequently, it is the weak H-(CHB11Cl11) BDE (70.0 kcal mol-1, G3(MP2)) compared to the strong BDE of (1-C4F9SO2)2N-H (127.4 ± 3.2 kcal mol-1) that accounts for the greater acidity of carborane acids.

  17. Different functions of intestinal and liver-type fatty acid-binding proteins in intestine and in whole body energy homeostasis

    OpenAIRE

    Lagakos, William Stacy; Gajda, Angela Marie; Agellon, Luis; Binas, Bert; Choi, Victor; Mandap, Bernadette; Russnak, Timothy; Zhou, Yin Xiu; Storch, Judith

    2011-01-01

    It has long been known that mammalian enterocytes coexpress two members of the fatty acid-binding protein (FABP) family, the intestinal FABP (IFABP) and the liver FABP (LFABP). Both bind long-chain fatty acids and have similar though not identical distributions in the intestinal tract. While a number of in vitro properties suggest the potential for different functions, the underlying reasons for expression of both proteins in the same cells are not known. Utilizing mice genetically lacking ei...

  18. 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.

  19. Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N.

    Science.gov (United States)

    Vorontsov, Ivan I; Miyashita, Osamu

    2011-04-30

    Complexes of two Cyanovirin-N (CVN) mutants, m4-CVN and P51G-m4-CVN, with deoxy di-mannose analogs were employed as models to generate conformational ensembles using explicit water Molecular Dynamics (MD) simulations in solution and in crystal environment. The results were utilized for evaluation of binding free energies with the molecular mechanics Poisson-Boltzmann (or Generalized Born) surface area, MM/PB(GB)SA, methods. The calculations provided the ranking of deoxy di-mannose ligands affinity in agreement with available qualitative experimental evidences. This confirms the importance of the hydrogen-bond network between di-mannose 3'- and 4'-hydroxyl groups and the protein binding site B(M) as a basis of the CVN activity as an effective HIV fusion inhibitor. Comparison of binding free energies averaged over snapshots from the solution and crystal simulations showed high promises in the use of the crystal matrix for acceleration of the conformational ensemble generation, the most time consuming step in MM/PB(GB)SA approach. Correlation between energy values based on solution versus crystal ensembles is 0.95 for both MM/PBSA and MM/GBSA methods. PMID:20949512

  20. 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.

  1. 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.)

  2. External electric field effect on exciton binding energy in InGaAsP/InP quantum wells%外电场对InGaAsP/InP量子阱内激子结合能的影响

    Institute of Scientific and Technical Information of China (English)

    王文娟; 王海龙; 龚谦; 宋志棠; 汪辉; 封松林

    2013-01-01

    Exciton binding energies in InGaAsP/InP quantum well with different contents of In are calculated through variational method in the effective mass approximation. The variation of exciton binding energy as a function of well width, In content, and applied external electric field is studied. It is shown that the exciton binding energy is a non-monotonic function of well width. It increases first until reaching a maximum, and then decreases as the well width increases farther. In addition, with the increase of In content, the well width should increase to reach the maximum value of exciton binding energy. It is also found that the external electric field has little effect on binding energy, but when the electric field is large enough, it will destroy the excitonic effect. These results may provide some theoretical basis for the design and control of InGaAsP/InP optical devices.%在有效质量近似下采用变分法计算了InGaAsP/InP量子阱内不同In组分下的激子结合能,分析了结合能随阱宽和In组分的变化情况,并且讨论了外加电场对激子结合能的影响。结果表明:激子结合能是阱宽的一个非单调函数,随阱宽的变化呈现先增加后减小的趋势;随着In组分增大,激子结合能达到最大值的阱宽相应变小,这与材料的带隙改变有关;在一定范围内电场的存在对激子结合能的影响很小,但电场强度较大时会破坏激子效应。

  3. Binding of Quasi-Two-Dimensional Biexcitons

    DEFF Research Database (Denmark)

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

    1996-01-01

    Biexciton binding in GaAs quantum wells has been investigated for a range of well thicknesses (80-160 Angstrom) with spectrally resolved photoluminescence and transient degenerate four-wave mixing. Both light and heavy hole biexcitons are observed. The ratio of the binding energy of the heavy hole...

  4. Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies.

    Science.gov (United States)

    Meher, Biswa Ranjan; Wang, Yixuan

    2012-02-16

    In the present work, the binding of inhibitor TMC114 (darunavir) to wild-type (WT), single (I50V) as well as double (I50L/A71V) mutant HIV-proteases (HIV-pr) was investigated with all-atom molecular dynamics (MD) simulations as well as molecular mechanic-Poisson-Boltzmann surface area (MM-PBSA) calculation. For both the apo and complexed HIV-pr, many intriguing effects due to double mutant, I50L/A71V, are observed. For example, the flap-flap distance and the distance from the active site to the flap residues in the apo I50L/A71V-HIV-pr are smaller than those of WT- and I50V-HIV-pr, probably making the active site smaller in volume and closer movement of flaps. For the complexed HIV-pr with TMC114, the double mutant I50L/A71V shows a less curling of the flap tips and less flexibility than WT and the single mutant I50V. As for the other previous studies, the present results also show that the single mutant I50V decreases the binding affinity of I50V-HIV-pr to TMC, resulting in a drug resistance; whereas the double mutant I50L/A71V increases the binding affinity, and as a result of the stronger binding, the I50L/A71V may be well adapted by the TMC114. The energy decomposition analysis suggests that the increase of the binding for the double mutant I50L/A71V-HIV-pr can be mainly attributed to the increase in electrostatic energy by -5.52 kacl/mol and van der Waals by -0.42 kcal/mol, which are canceled out in part by the increase of polar solvation energy of 1.99 kcal/mol. The I50L/A71V mutant directly increases the binding affinity by approximately -0.88 (Ile50 to Leu50) and -0.90 (Ile50' to Leu50') kcal/mol, accounting 45% for the total gain of the binding affinity. Besides the direct effects from the residues Leu50 and Leu50', the residue Gly49' increases the binding affinity of I50L/A71V-HIV-pr to the inhibitor by -0.74 kcal/mol, to which the electrostatic interaction of Leu50's backbone contributes by -1.23 kcal/mol. Another two residues Ile84 and Ile47' also

  5. 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.

  6. Skeletal muscle metabolic characteristics before and after energy restriction in human obesity: fibre type, enzymatic beta-oxidative capacity and fatty acid-binding protein content.

    OpenAIRE

    Kempen, K.P.G.; Saris, W.H.M.; Kuipers, H; Glatz, J.F.; van der Vusse, G. J.

    1998-01-01

    University of Maastricht, Maastricht, The Netherlands. BACKGROUND: Skeletal muscle has the ability to adapt as result of dietary, hormonal or pharmacological interventions affecting energy metabolism. The aim of the present study was to investigate the effects of energy restriction on skeletal muscle metabolic characteristics in obese women. METHODS: The effects of 8 weeks' energy restriction on body composition, energy expenditure and skeletal muscle characteristics were investigated in 28 h...

  7. 补体蛋白C3c与抑制剂Compstatin的结合自由能计算%Binding free energy calculation of complement protein C3c-inhibitor Compstatin interaction by MM/PBSA method

    Institute of Scientific and Technical Information of China (English)

    杨威; 张峰; 马志; 郑俊峰

    2013-01-01

    The binding free energy of human C3c-Compstatin complex was calculated by an MM/PBS A method, and the key residues interactions were also investigated between MG4-MG5 binding domain of C3c and Compstatin by using energy decomposition method. The results showed that the calculated binding free energy ( - 8. 06 kcal/mol) was in high agreement with the binding affinity(-6.72 kcal/mol)- by the experimental essays, the total energy in the molecule( -177.24 kcal/mol) showing the maximal contribution to binding complement inhibitor, followed by vaccum electrostatic interaction(-108.74 kcal/mol)and Vander Waals interaction(-68.51 kcal/mol). The dynamic process of combination between C3c and the inhibitor together with the changes of the protein under the effect of combination was simulated as a complementary part in the crystal experiments. Our molecular dynamics stimulation proved the experiment with the structure information: Residue ARG459, ASP491, MET457 of C3c and TRP7,TRP4,HIS10 of Compstatin had major contribution to the binding free energy of the complex. The information above provides some insights into the based structural design of inhibitor of complement 3.%采用分子动力学模拟取样,运用MM-PBSA方法计算了人类C3c-Compstatin复合物的结合自由能.通过能量分解方法探究了人类补体蛋白C3c上抑制剂结合域MG4~MG5(巨球蛋白区域)上的主要残基与配体Compstatin纤维蛋白之间的相互作用和识别.结果表明:C3c与补体抑制剂Compstatin的理论结合自由能(-8.06 kcal/mol)与试验值(-6.72 kcal/mol)吻合较好,分子内能总和(-177.24 kcal/mol)对补体抵制剂的结合贡献最大,其次为真空静电作用能(-108.74 kcal/mol)和范德华作用能(-68.51kcal/mol).作为对结晶试验的补充,进行了C3c蛋白和小分子抑制剂之间结合的动态过程以及在两者结合的影响下蛋白形态变化的分子动力学模拟,结果发现C3c上的残基ARG459、ASP491、MET457

  8. Total iron binding capacity

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003489.htm Total iron binding capacity To use the sharing features on this page, please enable JavaScript. Total iron binding capacity (TIBC) is a blood test to ...

  9. Plant Hormone Binding Sites

    OpenAIRE

    Napier, Richard

    2004-01-01

    • Aims Receptors for plant hormones are becoming identified with increasing rapidity, although a frustrating number remain unknown. There have also been many more hormone‐binding proteins described than receptors. This Botanical Briefing summarizes what has been discovered about hormone binding sites, their discovery and descriptions, and will not dwell on receptor functions or activities except where these are relevant to understand binding.

  10. Analysis of binding heterogeneity.

    NARCIS (Netherlands)

    Nederlof, M.M.

    1992-01-01

    Binding heterogeneity, due to different functional groups on a reactive surface, plays an important role in the binding of small molecules or ions to many adsorbents, both in industrial processes and in natural environments. The binding heterogeneity is described by a distribution of affinity consta

  11. A model for positron binding to polar molecules

    CERN Document Server

    Gribakin, G F

    2015-01-01

    A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to unphysically small core radii for all of the molecules studied. This suggests that electron-positron correlations neglected in the simple model play a large role in determining the binding energy. We account for these by including polarization potential via perturbation theory. The improved model enables reliable predictions of binding energies to be made for a range of polar organic molecules and hydrogen cyanide, whose binding energy is known from accurate quantum chemistry calculations. The model explains the linear dependence of the binding energies on the polarizability inferred from the experimental data [Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203].

  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. 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

  14. 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.

  15. 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.

  16. Different functions of intestinal and liver-type fatty acid-binding proteins in intestine and in whole body energy homeostasis.

    Science.gov (United States)

    Lagakos, William Stacy; Gajda, Angela Marie; Agellon, Luis; Binas, Bert; Choi, Victor; Mandap, Bernadette; Russnak, Timothy; Zhou, Yin Xiu; Storch, Judith

    2011-05-01

    It has long been known that mammalian enterocytes coexpress two members of the fatty acid-binding protein (FABP) family, the intestinal FABP (IFABP) and the liver FABP (LFABP). Both bind long-chain fatty acids and have similar though not identical distributions in the intestinal tract. While a number of in vitro properties suggest the potential for different functions, the underlying reasons for expression of both proteins in the same cells are not known. Utilizing mice genetically lacking either IFABP or LFABP, we directly demonstrate that each of the enterocyte FABPs participates in specific pathways of intestinal lipid metabolism. In particular, LFABP appears to target fatty acids toward oxidative pathways and dietary monoacylglycerols toward anabolic pathways, while IFABP targets dietary fatty acids toward triacylglycerol synthesis. The two FABP-null models also displayed differences in whole body response to fasting, with LFABP-null animals losing less fat-free mass and IFABP-null animals losing more fat mass relative to wild-type mice. The metabolic changes observed in both null models appear to occur by nontranscriptional mechanisms, supporting the hypothesis that the enterocyte FABPs are specifically trafficking their ligands to their respective metabolic fates. PMID:21350192

  17. 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.

  18. 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 ...

  19. DNA Triplexes That Bind Several Cofactor Molecules.

    Science.gov (United States)

    Vollmer, Sven; Richert, Clemens

    2015-12-14

    Cofactors are critical for energy-consuming processes in the cell. Harnessing such processes for practical applications requires control over the concentration of cofactors. We have recently shown that DNA triplex motifs with a designed binding site can be used to capture and release nucleotides with low micromolar dissociation constants. In order to increase the storage capacity of such triplex motifs, we have explored the limits of ligand binding through designed cavities in the oligopurine tract. Oligonucleotides with up to six non-nucleotide bridges between purines were synthesized and their ability to bind ATP, cAMP or FAD was measured. Triplex motifs with several single-nucleotide binding sites were found to bind purines more tightly than triplexes with one large binding site. The optimized triplex consists of 59 residues and four C3-bridges. It can bind up to four equivalents of ligand with apparent Kd values of 52 µM for ATP, 9 µM for FAD, and 2 µM for cAMP. An immobilized version fuels bioluminescence via release of ATP at body temperature. These results show that motifs for high-density capture, storage and release of energy-rich biomolecules can be constructed from synthetic DNA. PMID:26561335

  20. Theoretical insight into the binding energy and detonation performance of ε-, γ-, β-CL-20 cocrystals with β-HMX, FOX-7, and DMF in different molar ratios, as well as electrostatic potential.

    Science.gov (United States)

    Feng, Rui-Zhi; Zhang, Shu-Hai; Ren, Fu-de; Gou, Rui-Jun; Gao, Li

    2016-06-01

    Molecular dynamics method was employed to study the binding energies on the selected crystal planes of the ε-, γ-, β-conformation 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (ε-, γ-, β-CL-20) cocrystal explosives with 1,1-diamino-2,2-dinitroethylene (FOX-7), 1,3,5,7-tetranitro- 1,3,5,7-tetrazacyclooctane with β-conformation (β-HMX) and N,N-dimethylformamide (DMF) in different molar ratios. The oxygen balance, density, detonation velocity, detonation pressure, and surface electrostatic potential were analyzed. The results indicate that the binding energies E b (*) and stabilities are in the order of 1:1 > 2:1 > 3:1 > 5:1 > 8:1 (CL-20:FOX-7/β-HMX/DMF). The values of E b (*) and stabilities of the energetic-nonenergetic CL-20/DMF cocrystals are far larger than those of the energetic-energetic CL-20/FOX-7 and CL-20/β-HMX, and those of CL-20/β-HMX are the smallest. For CL-20/FOX-7 and CL-20/β-HMX, the largest E b (*) appears in the cocrystals with the 1:1, 1:2 or 1:3 molar ratio, and the stabilities of the cocrystals with the excess ratio of CL-20 are weaker than those in the cocrystals with the excess ratio of FOX-7 or β-HMX. In CL-20/FOX-7, CL-20 prefers adopting the γ-form, and ε-CL-20 is the preference in CL-20/β-HMX, and ε-CL-20 and β-CL-20 can be found in CL-20/DMF. The CL-20/FOX-7 and CL-20/β-HMX cocrystals with low molar ratios can meet the requirements of low sensitive high energetic materials. Surface electrostatic potential reveals the nature of the sensitivity change upon the cocrystal formation. Graphical Abstract MD method was employed to study the binding energies on the selected crystal planes in the ε-, γ-, β-CL-20 cocrystals with FOX-7, β-HMX and DMF in different molar ratios. Surface electrostatic potential reveals the nature of the sensitivity change in cocrystals. PMID:27168198

  1. 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

  2. Photonic Binding in Silicon-Colloid Microcavities

    OpenAIRE

    Xifré-Pérez, E.; García de Abajo, Francisco Javier; Fenollosa Esteve, Roberto; Meseguer, Francisco

    2009-01-01

    Photonic binding between two identical silicon-colloid-based microcavities is studied by using a generalized multipolar expansion. In contrast with previous works, we focus on low-order cavity modes that resemble low-energy electronic orbitals. For conservative light intensities, the interaction between cavity modes with moderate Q factors produces extremely large particle acceleration values. Optical forces dominate over vanderWaals, gravity, and Brownian motion, and they show a binding-anti...

  3. 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

  4. 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.

  5. Protein-protein binding affinities calculated using the LIE method

    OpenAIRE

    Andberg, Tor Arne Heim

    2011-01-01

    Absolute binding free energies for the third domain of the turkey ovomucoid inhibitor in complex with Streptomyces griseus proteinase B and porcine pancreatic elastase has been calculated using the linear interaction energy method.

  6. 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

  7. 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.

  8. 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)

  9. 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.

  10. Effect of peripartum dietary energy supplementation on thyroid hormones, insulin-like growth factor-i and its binding proteins in early lactation dairy cows

    Directory of Open Access Journals (Sweden)

    Kirovski Danijela

    2012-01-01

    Full Text Available The objective of this study was to examine the effect of dietary energy supplementation on hormones that are considered to be the main signals of a shift in energy balance around parturition. Sixty dry cows, 15 days before calving, were chosen and divided into two eaqual groups: control and experimental (GLY. Both groups were fed a standard ration balanced in accordance to the stage of the productivereproductive cycle. Additionally, each cow in the GLY group was given glycerol based dietary energy supplementation (250 mL daily during the dry and 300 mL daily during the lactation period, which provided additional 9.30 MJ NEL during the dry and 13.95 MJ NEL during the early lactation period. Milk production was measured on days 30 and 60 of lactation and milk production was significantly higher in GLY compared to control group at day 60 of lactation (p<0.05. Service period and insemination index were used as reproductive outcome parameters. Average service period in the control group was significantly longer than in the GLY group (p<0.05. Average insemination index in the control group was not significantly different than the index obtained for the GLY group. Blood samples were taken before the begining of the experiment (15 days before parturition, and at days 7, 30 and 60 of lactation. Concentrations of thyroid hormones, IGF-I, relative abundance of IGFBP-2, IGFBP-3 and IGFBP-4, concentrations of total protein and albumin in the blood were measured. Results showed that at days 7 and 30 after parturition, T4 concentrations were significantly higher (p<0.001, respectively in GLY than in the control group, while T3 concentrations were significantly higher in GLY group only at day 7 after parturition (p<0.001. IGF-I concentrations and IGFBP-3 abundance were significantly higher in the GLY compared to the control group in all three examined postpartum periods. IGFBP-2 and IGFBP-4 concentrations were higher in GLY compared to the control group in all

  11. Influence of different liquid-drop-based bindings on lighter mass fragments and entropy production

    Science.gov (United States)

    Kumar, Rohit; Shivani; Gautam, Sakshi

    2016-04-01

    We study the production of lighter fragments and associated phenomena within the Quantum Molecular Dynamics (QMD) model. The Minimum Spanning Tree (MST) method is used to identify the pre-clusters. The final stable fragments were identified by imposing binding energy criteria on the fragments formed using the MST method. The effect of different binding energy criteria was investigated by employing various liquid-drop-based binding energy formulae. Though light clusters show significant effect of different binding energies, their associated phenomenon, i.e. entropy production is insensitive towards different binding energy criteria.

  12. Influence of different liquid-drop-based bindings on lighter mass fragments and entropy production

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Rohit; Shivani; Gautam, Sakshi [Panjab University, Department of Physics, Chandigarh (India)

    2016-04-15

    We study the production of lighter fragments and associated phenomena within the Quantum Molecular Dynamics (QMD) model. The Minimum Spanning Tree (MST) method is used to identify the pre-clusters. The final stable fragments were identified by imposing binding energy criteria on the fragments formed using the MST method. The effect of different binding energy criteria was investigated by employing various liquid-drop-based binding energy formulae. Though light clusters show significant effect of different binding energies, their associated phenomenon, i.e. entropy production is insensitive towards different binding energy criteria. (orig.)

  13. Protein-ligand binding affinities from large-scale quantum mechanical simulations

    OpenAIRE

    Fox, Stephen J.

    2012-01-01

    The accurate prediction of protein-drug binding affinities is a major aim of computational drug optimisation and development. A quantitative measure of binding affinity is provided by the free energy of binding, and such calculations typically require extensive configurational sampling of entities such as proteins with thousands of atoms. Current binding free energy methods use force fields to perform the configurational sampling and to compute interaction energies. Due to the empirical natur...

  14. 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.

  15. 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 ...

  16. Energy

    International Nuclear Information System (INIS)

    This chapter of the environmental control report deals with the environmental impact of energy production, energy conversion, atomic energy and renewable energy. The development of the energy consumption in Austria for the years 1993 to 1999 is given for the different energy types. The development of the use of renewable energy sources in Austria is given, different domestic heat-systems are compared, life cycles and environmental balance are outlined. (a.n.)

  17. Binding of calcium and carbonate to polyacrylates.

    Science.gov (United States)

    Tribello, Gareth A; Liew, CheeChin; Parrinello, Michele

    2009-05-21

    Polyacrylate molecules can be used to slow the growth of calcium carbonate. However, little is known about the mechanism by which the molecules impede the growth rate. A recent computational study (Bulo et al. Macromolecules 2007, 40, 3437) used metadynamics to investigate the binding of calcium to polyacrylate chains and has thrown some light on the coiling and precipitation of these polymers. We extend these simulations to examine the binding of calcium and carbonate to polyacrylate chains. We show that calcium complexed with both carbonate and polyacrylate is a very stable species. The free energies of calcium-carbonate-polyacrylate complexes, with different polymer configurations, are calculated, and differences in the free energy of the binding of carbonate are shown to be due to differences in the amount of steric hindrance about the calcium, which prevents the approach of the carbonate ion. PMID:19400592

  18. 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

  19. 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.

  20. 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...

  1. Cellulose binding domain proteins

    Energy Technology Data Exchange (ETDEWEB)

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

    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.

  2. 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.

  3. Lectin binding in meningiomas.

    Science.gov (United States)

    Kleinert, R; Radner, H

    1987-01-01

    Forty-two meningiomas of different morphological sub-type were examined to determine their pattern of binding to 11 different lectins which characterize cell surface components such as carbohydrate residues. Histiocytic and xanthoma cells within meningiomas could be demonstrated with six different lectins: wheat germ agglutinin (WGA), peanut agglutinin (PNA) Bauhinia purpurea agglutinin (BPA), Helix pomatia agglutinin (HPA), Vicia fava agglutinin (VFA) and Soyabean agglutinin (SBA). Vascular elements including endothelial cells and intimal cells, bound Ulex europaeus agglutinin type 1 (UEA 1), WGA and HPA. The fibrous stroma in fibrous and fibroblastic meningiomas bound PNA, Laburnum alpinum agglutinin (LAA) and SBA. Tumour cells in meningotheliomatous meningiomas and some areas of anaplastic meningiomas bound Concanavalin A, PNA, LAA and VFA whereas tumour cells in fibrous and fibroblastic meningiomas bound BPA, LAA and VFA. Lectin binding has proved to be of value in detecting histiocytic and xanthoma cells together with vascular elements within meningiomas. In addition, the different lectin binding patterns allow different histological sub-types of meningioma to be distinguished although the biological significance of the binding patterns is unclear. PMID:3658105

  4. 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

  5. Concentration-dependent Cu(II) binding to prion protein

    Science.gov (United States)

    Hodak, Miroslav; Lu, Wenchang; Bernholc, Jerry

    2008-03-01

    The prion protein plays a causative role in several neurodegenerative diseases, including mad cow disease in cattle and Creutzfeldt-Jakob disease in humans. The normal function of the prion protein is unknown, but it has been linked to its ability to bind copper ions. Experimental evidence suggests that copper can be bound in three distinct modes depending on its concentration, but only one of those binding modes has been fully characterized experimentally. Using a newly developed hybrid DFT/DFT method [1], which combines Kohn-Sham DFT with orbital-free DFT, we have examined all the binding modes and obtained their detailed binding geometries and copper ion binding energies. Our results also provide explanation for experiments, which have found that when the copper concentration increases the copper binding mode changes, surprisingly, from a stronger to a weaker one. Overall, our results indicate that prion protein can function as a copper buffer. 1. Hodak, Lu, Bernholc, JCP, in press.

  6. AB-Bind: Antibody binding mutational database for computational affinity predictions.

    Science.gov (United States)

    Sirin, Sarah; Apgar, James R; Bennett, Eric M; Keating, Amy E

    2016-02-01

    Antibodies (Abs) are a crucial component of the immune system and are often used as diagnostic and therapeutic agents. The need for high-affinity and high-specificity antibodies in research and medicine is driving the development of computational tools for accelerating antibody design and discovery. We report a diverse set of antibody binding data with accompanying structures that can be used to evaluate methods for modeling antibody interactions. Our Antibody-Bind (AB-Bind) database includes 1101 mutants with experimentally determined changes in binding free energies (ΔΔG) across 32 complexes. Using the AB-Bind data set, we evaluated the performance of protein scoring potentials in their ability to predict changes in binding free energies upon mutagenesis. Numerical correlations between computed and observed ΔΔG values were low (r = 0.16-0.45), but the potentials exhibited predictive power for classifying variants as improved vs weakened binders. Performance was evaluated using the area under the curve (AUC) for receiver operator characteristic (ROC) curves; the highest AUC values for 527 mutants with |ΔΔG| > 1.0 kcal/mol were 0.81, 0.87, and 0.88 using STATIUM, FoldX, and Discovery Studio scoring potentials, respectively. Some methods could also enrich for variants with improved binding affinity; FoldX and Discovery Studio were able to correctly rank 42% and 30%, respectively, of the 80 most improved binders (those with ΔΔG < -1.0 kcal/mol) in the top 5% of the database. This modest predictive performance has value but demonstrates the continuing need to develop and improve protein energy functions for affinity prediction. PMID:26473627

  7. 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...

  8. Computational design of a PAK1 binding protein.

    Science.gov (United States)

    Jha, Ramesh K; Leaver-Fay, Andrew; Yin, Shuangye; Wu, Yibing; Butterfoss, Glenn L; Szyperski, Thomas; Dokholyan, Nikolay V; Kuhlman, Brian

    2010-07-01

    We describe a computational protocol, called DDMI, for redesigning scaffold proteins to bind to a specified region on a target protein. The DDMI protocol is implemented within the Rosetta molecular modeling program and uses rigid-body docking, sequence design, and gradient-based minimization of backbone and side-chain torsion angles to design low-energy interfaces between the scaffold and target protein. Iterative rounds of sequence design and conformational optimization were needed to produce models that have calculated binding energies that are similar to binding energies calculated for native complexes. We also show that additional conformation sampling with molecular dynamics can be iterated with sequence design to further lower the computed energy of the designed complexes. To experimentally test the DDMI protocol, we redesigned the human hyperplastic discs protein to bind to the kinase domain of p21-activated kinase 1 (PAK1). Six designs were experimentally characterized. Two of the designs aggregated and were not characterized further. Of the remaining four designs, three bound to the PAK1 with affinities tighter than 350 muM. The tightest binding design, named Spider Roll, bound with an affinity of 100 muM. NMR-based structure prediction of Spider Roll based on backbone and (13)C(beta) chemical shifts using the program CS-ROSETTA indicated that the architecture of human hyperplastic discs protein is preserved. Mutagenesis studies confirmed that Spider Roll binds the target patch on PAK1. Additionally, Spider Roll binds to full-length PAK1 in its activated state but does not bind PAK1 when it forms an auto-inhibited conformation that blocks the Spider Roll target site. Subsequent NMR characterization of the binding of Spider Roll to PAK1 revealed a comparably small binding 'on-rate' constant (design the site of novel protein-protein interactions is an important step towards creating new proteins that are useful as therapeutics or molecular probes.

  9. Energy.

    Science.gov (United States)

    Chambers, David W

    2012-01-01

    Energy is the capacity to do the things we are capable of and desire to accomplish. Most often this is thought of in terms of PEP--personal energy potential--a reservoir of individual vivacity and zest for work. Like a battery, energy can be conceived of as a resource that is alternatively used and replenished. Transitions between activities, variety of tasks, and choices of what to spend energy on are part of energy management. Energy capacity can be thought of at four levels: (a) so little that harm is caused and extraordinary steps are needed for recovery, (b) a deficit that slightly impairs performance but will recover naturally, (c) the typical range of functioning, and (d) a surplus that may or may not be useful and requires continual investment to maintain. "Flow" is the experience of optimal energy use when challenges balance capacity as a result of imposing order on our environment. There are other energy resources in addition to personal vim. Effective work design reduces demands on energy. Money, office design, and knowledge are excellent substitutes for personal energy. PMID:22856055

  10. Binding of helium to metallic impurities in tungsten. Experiments and computer simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kolk, G.J. van; Veen, A. van; Caspers, L.M. (Interuniversitair Reactor Inst., Delft (Netherlands)); Hosson, J.T.M. (Rijksuniversiteit Groningen (Netherlands). Materials Science Centre)

    1985-01-01

    A W(100) single crystal was implanted with low doses Ag, Cu, Mn, Cr, Al or In. Subsequent heating to 1600 K removed all vacancies and left the implants in substitutional positions. Low energy He was injected, and binding of He to the substitutional impurities was observed. Binding energies were found as high as 1.25 eV for one He atom. Pair potential calculations were performed; the calculated binding energies correspond reasonably with the measured ones.

  11. 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.

  12. 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...... to express high levels of megalin, is inhibitable by excess unlabeled FBP and by receptor associated protein, a known inhibitor of binding to megalin. Immortalized rat yolk sac cells, representing an established model for studying megalin-mediated uptake, reveal (125)I-labeled FBP uptake which is inhibited...

  13. 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.

  14. Structural modeling for DNA binding to antioxidants resveratrol, genistein and curcumin.

    Science.gov (United States)

    N'soukpoé-Kossi, C N; Bourassa, P; Mandeville, J S; Bekale, L; Tajmir-Riahi, H A

    2015-10-01

    Several models are presented here for the bindings of the antioxidant polyphenols resveratrol, genistein and curcumin with DNA in aqueous solution at physiological conditions. Multiple spectroscopic methods and molecular modeling were used to locate the binding sites of these polyphenols with DNA duplex. Structural models showed that intercalation is more stable for resveratrol and genistein than groove bindings, while curcumin interaction is via DNA grooves. Docking showed more stable complexes formed with resveratrol and genistein than curcumin with the free binding energies of -4.62 for resveratrol-DNA (intercalation), -4.28 for resveratrol-DNA (groove binding), -4.54 for genistein-DNA (intercalation), -4.38 for genistein-DNA (groove binding) and -3.84 kcal/mol for curcumin-DNA (groove binding). The free binding energies show polyphenol-DNA complexation is spontaneous at room temperature. At high polyphenol concentration a major DNA aggregation occurred, while biopolymer remained in B-family structure. PMID:26188387

  15. Exploration of the binding mode between (-)-zampanolide and tubulin using docking and molecular dynamics simulation.

    Science.gov (United States)

    Liao, Si-Yan; Mo, Guang-Quan; Chen, Jin-Can; Zheng, Kang-Cheng

    2014-02-01

    The binding mode of (-)-zampanolide (ZMP) to tubulin was investigated using docking, molecular dynamics (MD) simulation, and binding free-energy calculations. The docking studies validated the experimental results indicating that the paclitaxel site is the binding site for (-)-ZMP. The 18 ns MD simulation shows the docking mode has changed a lot, whereas it offers more reliable binding data. MM-PBSA binding free-energy calculations further confirmed the results of the MD simulation. The study revealed that hydrophobic interactions play an important role in stabilizing the binding, and the strong hydrogen bond formed with Asp224 enhances the affinity for tubulin. Meanwhile, the results support the assumption that (-)-ZMP can be attacked by His227, leading to a nucleophilic reaction and covalent binding. These theoretical results lead to a greater understanding of the mechanism of action of binding to tubulin, and will therefore aid the design of new compounds with higher affinities for tubulin. PMID:24478043

  16. 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.

  17. 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.

  18. 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...

  19. Enthalpy/entropy compensation effects from cavity desolvation underpin broad ligand binding selectivity for rat odorant binding protein 3.

    Science.gov (United States)

    Portman, Katherine L; Long, Jed; Carr, Stephen; Briand, Loïc; Winzor, Donald J; Searle, Mark S; Scott, David J

    2014-04-15

    Evolution has produced proteins with exquisite ligand binding specificity, and manipulating this effect has been the basis for much of modern rational drug design. However, there are general classes of proteins with broader ligand selectivity linked to function, the origin of which is poorly understood. The odorant binding proteins (OBPs) sequester volatile molecules for transportation to the olfactory receptors. Rat OBP3, which we characterize by X-ray crystallography and NMR, binds a homologous series of aliphatic γ-lactones within its aromatic-rich hydrophobic pocket with remarkably little variation in affinity but extensive enthalpy/entropy compensation effects. We show that the binding energetics are modulated by two desolvation processes with quite different thermodynamic signatures. Ligand desolvation follows the classical hydrophobic effect; however, cavity desolvation is consistent with the liberation of "high energy" water molecules back into bulk solvent with a strong, but compensated, enthalpic contribution, which together underpin the origins of broad ligand binding selectivity.

  20. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

    Science.gov (United States)

    Wickstrom, Lauren; Deng, Nanjie; He, Peng; Mentes, Ahmet; Nguyen, Crystal; Gilson, Michael K; Kurtzman, Tom; Gallicchio, Emilio; Levy, Ronald M

    2016-01-01

    Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand binding, organic host-guest complexes have long served as models for both experimental and computational studies because of the abundance of binding affinity data available for such systems. Binding affinity data collected for cyclodextrin (CD) inclusion complexes, a popular model for molecular recognition, is potentially a more reliable resource for tuning energy parameters than hydration free energy measurements. Convergence of binding free energy calculations on CD host-guest systems can also be obtained rapidly, thus offering the opportunity to assess the robustness of these parameters. In this work, we demonstrate how implicit solvent parameters can be developed using binding affinity experimental data and the binding energy distribution analysis method (BEDAM) and validated using the Grid Inhomogeneous Solvation Theory analysis. These new solvation parameters were used to study protein-ligand binding in two drug targets against the HIV-1 virus and improved the agreement between the calculated and the experimental binding affinities. This work illustrates how benchmark sets of high quality experimental binding affinity data and physics-based binding free energy models can be used to evaluate and optimize force fields for protein-ligand systems. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26256816

  1. Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

    International Nuclear Information System (INIS)

    Highlights: • Energetics of the interaction of proflavine with DNA has been studied. • The binding reaction was favored by both negative enthalpy and positive entropy. • Enthalpy–entropy compensation phenomenon was observed. • Non-polyelectrolytic forces played a dominant role in the binding process. • Proflavine enhanced the thermal stability of DNA remarkably. - Abstract: The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 105 · M−1 at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation

  2. 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.

  3. Alcohol Binding to the Odorant Binding Protein LUSH: Multiple Factors Affecting Binding Affinities

    OpenAIRE

    Ader, Lauren; Jones, David N. M.; Lin, Hai

    2010-01-01

    Density function theory (DFT) calculations have been carried out to investigate the binding of alcohols to the odorant binding protein LUSH from Drosophila melanogaster. LUSH is one of the few proteins known to bind to ethanol at physiologically relevant concentrations and where high-resolution structural information is available for the protein bound to alcohol at these concentrations. The structures of the LUSH–alcohol complexes identify a set of specific hydrogen-bonding interactions as cr...

  4. 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).

  5. 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

  6. 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)

  7. 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.

  8. [3]tetrahydrotrazodone binding. Association with serotonin binding sites

    International Nuclear Information System (INIS)

    High (17 nM) and low (603 nM) affinity binding sites for [3]tetrahydrotrazodone ([3] THT), a biologically active analogue of trazodone, have been identified in rat brain membranes. The substrate specificity, concentration, and subcellular and regional distributions of these sites suggest that they may represent a component of the serotonin transmitter system. Pharmacological analysis of [3]THT binding, coupled with brain lesion and drug treatment experiments, revealed that, unlike other antidepressants, [3] THT does not attach to either a biogenic amine transporter or serotonin binding sites. Rather, it would appear that [3]THT may be an antagonist ligand for the serotonin binding site. This probe may prove of value in defining the mechanism of action of trazodone and in further characterizing serotonin receptors

  9. Relative Binding Affinities of Monolignols to Horseradish Peroxidase.

    Science.gov (United States)

    Sangha, Amandeep K; Petridis, Loukas; Cheng, Xiaolin; Smith, Jeremy C

    2016-08-11

    Monolignol binding to the peroxidase active site is the first step in lignin polymerization in plant cell walls. Using molecular dynamics, docking, and free energy perturbation calculations, we investigate the binding of monolignols to horseradish peroxidase C. Our results suggest that p-coumaryl alcohol has the strongest binding affinity followed by sinapyl and coniferyl alcohol. Stacking interactions between the monolignol aromatic rings and nearby phenylalanine residues play an important role in determining the calculated relative binding affinities. p-Coumaryl and coniferyl alcohols bind in a pose productive for reaction in which a direct H-bond is formed between the phenolic -OH group and a water molecule (W2) that may facilitate proton transfer during oxidation. In contrast, in the case of sinapyl alcohol there is no such direct interaction, the phenolic -OH group instead interacting with Pro139. Since proton and electron transfer is the rate-limiting step in monolignol oxidation by peroxidase, the binding pose (and thus the formation of near attack conformation) appears to play a more important role than the overall binding affinity in determining the oxidation rate. PMID:27447548

  10. 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.

  11. 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.

  12. Binding modes of thrombin binding aptamers investigated by simulations and experiments

    Science.gov (United States)

    Trapaidze, A.; Bancaud, A.; Brut, M.

    2015-01-01

    Thrombin binding aptamers HD1 and HD22 are the most studied aptamers, both for therapeutic and sensing purposes. Yet, there is still no commercialized aptamer-based sensor device for thrombin detection, suggesting that the binding modes of these aptamers remain to be precisely described. Here, we investigate thrombin-aptamer interactions with molecular dynamics simulations, and show that the different solved structures of HD1-thrombin complex are energetically similar and consequently possibly co-existing. Conversely, HD22 folding is much more stable, and its binding energy with thrombin is significantly larger than that of HD1 complexes. These results are confronted to experiments, which consist in monitoring aggregation of aptamer-functionalized gold nanoparticles triggered by thrombin. HD1 alone, but not HD22, can trigger aggregation, meaning that this aptamer has multiple sites of interactions with thrombin. Furthermore, pre-incubation of HD22 with thrombin impedes HD1 aggregation, suggesting that HD1 and HD22 have competing affinities for the same binding site. Altogether, this study shows that the characterization of aptamer-thrombin interactions by structural and kinetic experiments joined to simulations is necessary for the development of biosensors.

  13. 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.

  14. Interaction of I50V Mutant and I50L/A71V Double Mutant HIV-protease with Inhibitor TMC114 (Darunavir): Molecular Dynamics Simulation and Binding Free Energy Studies

    OpenAIRE

    Meher, Biswa Ranjan; Wang, Yixuan

    2012-01-01

    In the present work the binding of inhibitor TMC114 (darunavir) to wild type (WT), single (I50V) as well as double (I50L/A71V) mutant HIV-proteases (HIV-pr) was investigated with all-atom molecular dynamics (MD) simulations as well as molecular mechanic-Poisson Boltzmann surface area (MM-PBSA) calculation. For both the apo and complexed HIV-pr, many intriguing effects due to double mutant, I50L/A71V, are observed. For example, the flap-flap distance and the distance from the active site to th...

  15. Structural studies of sugar binding proteins

    OpenAIRE

    Sooriyaarachchi, Sanjeewani

    2010-01-01

    Binding proteins, which are themselves non-enzymatic, play an important role in enzymatic reactions as well as non-enzymatic processes by providing a binding platform for the specific recognition of particular molecules. For example, periplasmic binding proteins play a vital role in nutrient uptake in Gram-negative bacteria. In the present study, three sugar binding proteins, including two periplasmic binding proteins and a β-glucan binding protein, are described. The glucose/galactose bindin...

  16. Binding modes of peptidomimetics designed to inhibit STAT3.

    Directory of Open Access Journals (Sweden)

    Ankur Dhanik

    Full Text Available STAT3 is a transcription factor that has been found to be constitutively activated in a number of human cancers. Dimerization of STAT3 via its SH2 domain and the subsequent translocation of the dimer to the nucleus leads to transcription of anti-apoptotic genes. Prevention of the dimerization is thus an attractive strategy for inhibiting the activity of STAT3. Phosphotyrosine-based peptidomimetic inhibitors, which mimic pTyr-Xaa-Yaa-Gln motif and have strong to weak binding affinities, have been previously investigated. It is well-known that structures of protein-inhibitor complexes are important for understanding the binding interactions and designing stronger inhibitors. Experimental structures of inhibitors bound to the SH2 domain of STAT3 are, however, unavailable. In this paper we describe a computational study that combined molecular docking and molecular dynamics to model structures of 12 peptidomimetic inhibitors bound to the SH2 domain of STAT3. A detailed analysis of the modeled structures was performed to evaluate the characteristics of the binding interactions. We also estimated the binding affinities of the inhibitors by combining MMPB/GBSA-based energies and entropic cost of binding. The estimated affinities correlate strongly with the experimentally obtained affinities. Modeling results show binding modes that are consistent with limited previous modeling studies on binding interactions involving the SH2 domain and phosphotyrosine(pTyr-based inhibitors. We also discovered a stable novel binding mode that involves deformation of two loops of the SH2 domain that subsequently bury the C-terminal end of one of the stronger inhibitors. The novel binding mode could prove useful for developing more potent inhibitors aimed at preventing dimerization of cancer target protein STAT3.

  17. Vacancy binding to substitutional silver in tungsten observed with thermal helium desorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    van der Kolk, G.J.; van Veen, A.; Caspers, L.M. (Technische Hogeschool Delft (Netherlands); Interuniversitair Reactor Inst., Delft (Netherlands)); de Hosson, J.T.M. (Materials Science Centre, Groningen (Netherlands))

    1983-04-01

    Low doses silver with energies between 5 and 25 keV were implanted in a (100) tungsten single crystal. The silver-vacancy complexes remaining after subsequent annealing were studied with thermal helium desorption spectrometry. The results show that the binding energy of one vacancy to substitutional silver is 0.8 +- 0.3 eV, and that additional vacancies are more strongly bound. The binding energy of He to substitutional silver increased with increasing filling degree.

  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. The use of isothermal titration calorimetry to determine the thermodynamics of metal ion binding to low-cost sorbents

    International Nuclear Information System (INIS)

    The thermodynamics of Al3+, Cr3+, and Pb2+ binding to the abundant biopolymer chitin have been determined using isothermal titration calorimetry (ITC) and compared to what is observed for binding to activated carbon. The use of ITC enables the detection of two distinct binding sites on chitin for all three metal ions. For the relative strong binding sites, free energy changes ranges from -37.6 kJ/mol to -41.8 kJ/mol while the same values are from -30.1 kJ/mol to -31.8 kJ/mol for the relative weak binding sites. All binding reactions to chitin are entropically driven. Interactions of the metal ions to activated carbon are best fitted as a single-site binding with relative weak binding with free energy changes from -26.3 kJ/mol to -26.8 kJ/mol.

  20. Competitive binding of transcription factors drives Mendelian dominance in regulatory genetic pathways

    OpenAIRE

    Porter, Adam H.; Johnson, Norman A.; Tulchinsky, Alexander Y.

    2016-01-01

    We report a new mechanism for allelic dominance in regulatory genetic interactions that we call binding dominance. We investigated a biophysical model of gene regulation, where the fractional occupancy of a transcription factor (TF) on the cis-regulated promoter site it binds to is determined by binding energy (-{\\Delta}G) and TF concentration. Transcription and gene expression proceed when the TF is bound to the promoter. In diploids, individuals may be heterozygous at the cis-site, at the T...

  1. State vector evolution localized over the edges of a square tight-binding lattice

    Institute of Scientific and Technical Information of China (English)

    He Liang-Ming; Shi Duan-Wen

    2009-01-01

    We study the time evolution of a state vector in a square tight-binding lattice, focusing on its evolution localized over the system surfaces. In this tight-binding lattice, the energy of atomic orbital centred at surface site is different from that at the interior (bulky) site by an energy shift U. It is shown that for the state vector initially localized on a surface, there exists an exponential law (y = aex/b + yo) determined by the absolute value of the energy shift, \\U\\, which describes the transition of the state evolving on the square tight-binding lattice, from delocalized over the whole lattice to localized over the surfaces.

  2. 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 ...

  3. [Spectroscopic studies on the binding of phenazopyridine hydrochloride and bovine serum albumin].

    Science.gov (United States)

    Zhou, Hong; Chen, Chang-Yun; Xie, An-Jian

    2007-09-01

    The binding of phenazopyridine hydrochloride and bovine serum albumin under physiological conditions was studied by spectroscopic method. The quenching mechanism of the fluorescence of bovine serum albumin by phenazopyridine hydrochloride was studied with fluorescence and absorption spectroscopy. The binding constant Kb and the number of binding sites n were determined at different temperatures according to Scatchard equation, and the main binding force was discussed by thermodynamic equations. The effect of the drug on bovine serum albumin conformation was also studied by using synchronous fluorescence spectroscopy. The quenching mechanism of phenazopyridine hydrochloride to bovine serum albumin is static quenching and non-radiation energy transfer. The binding constants Kb at 15, 25 and 37 degrees C are 2.47 x 10(7), 9.15 x 10(6) and 4.36 x 10(6) mol(-1) with one binding site, respectively. The thermodynamic parameters of the reaction are DeltaH = -71.2 kJ x mol(-1), and DeltaS = 124.8 J x mol(-1) x K(-1). Binding phenazopyridine hydrochloride to bovine serum albumin is a spontaneous inter-molecular interaction in which entropy increases and Gibbs free energy decreases. The binding distance r between phenazopyridine hydrochloride and bovine serum albumin is 1.61 nm according to Forster theory of non-radiation energy transfer. The binding force is electrostatic interaction. Phenazopyridine hydrochloride can be deposited and transported by serum protein in vivo. Phenazopyridine hydrochloride does affect the serum protein conformation. PMID:18051539

  4. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI).

    Science.gov (United States)

    Su, Pin-Chih; Tsai, Cheng-Chieh; Mehboob, Shahila; Hevener, Kirk E; Johnson, Michael E

    2015-09-30

    To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM-PBSA, MM-GBSA, and QM/MM-GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM-GBSA using 6 ns MD simulation trajectories together with GB(neck2) , PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r(2)  = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called "multiple independent sampling"), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB(HCT) and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r(2)  = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive "multiple independent sampling method" may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM-P(G)BSA were limited to inhibitors' relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program. PMID:26216222

  5. 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.

  6. Acid Gas Capture Using CO2-Binding Organic Liquids

    Energy Technology Data Exchange (ETDEWEB)

    Heldebrant, David J.; Koech, Phillip K.; Rainbolt, James E.; Zheng, Feng

    2010-11-10

    Current chemical CO2 scrubbing technology is primarily aqueous alkanolamine based. These systems rapidly bind CO2 (forming water-soluble carbamate and bicarbonate salts) however, the process has serious disadvantages. The concentration of monoethanolamine rarely exceeds 30 wt % due to the corrosive nature of the solution, and this reduces the maximum CO2 volumetric (≤108 g/L) and gravimetric capacity (≤7 wt%) of the CO2 scrubber. The ≤30 wt % loading of ethanolamine also means that a large excess of water must be pumped and heated during CO2 capture and release, and this greatly increases the energy requirements especially considering the high specific heat of water (4 j/g-1K-1). Our approach is to switch to organic systems that chemically bind CO2 as liquid alkylcarbonate salts. Our CO2-binding organic liquids have higher CO2 solubility, lower specific heats, potential for less corrosion and lower binding energies for CO2 than aqueous systems. CO2BOLs also reversibly bind and release mixed sulfur oxides. Furthermore the CO2BOL system can be direct solvent replacements for any solvent based CO2 capture systems because they are commercially available reagents and because they are fluids they would not require extensive process re-engineering.

  7. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen;

    2012-01-01

    profile of the integrin-linked kinase associated phosphatase (ILKAP), a member of the protein phosphatase 2C (PP2C) family. Phosphatases can potentially dephosphorylate these phosphopeptide substrates but, interestingly, performing the binding studies at 4 °C allowed efficient binding to phosphopeptides...... 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.......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...

  8. Water binding in legume seeds

    Science.gov (United States)

    Vertucci, C. W.; Leopold, A. C.

    1987-01-01

    The physical status of water in seeds has a pivotal role in determining the physiological reactions that can take place in the dry state. Using water sorption isotherms from cotyledon and axis tissue of five leguminous seeds, the strength of water binding and the numbers of binding sites have been estimated using van't Hoff analyses and the D'Arcy/Watt equation. These parameters of water sorption are calculated for each of the three regions of water binding and for a range of temperatures. Water sorption characteristics are reflective of the chemical composition of the biological materials as well as the temperature at which hydration takes place. Changes in the sorption characteristics with temperature and hydration level may suggest hydration-induced structural changes in cellular components.

  9. 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.

  10. 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.

  11. Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: analysis of flap dynamics and binding mechanism.

    Science.gov (United States)

    Meher, Biswa Ranjan; Wang, Yixuan

    2012-09-01

    Most of the currently treated HIV-1 protease (HIV-PR) inhibitors have been prone to suffer from the mutations associated drug resistance. Therefore, it is necessary to search for potent alternatives against the drug resistance. In the current study we have tested the single-walled carbon nanotube (SWCNT) as an inhibitor in wild type (WT) as well as in three primary mutants (I50V(PR), V82A(PR) and I84V(PR)) of the HIV-1-PR through docking the SWCNT in the active site region, and then performed all-atom MD simulations for the complexes. The conformational dynamics of HIV-PR with a 20 ns trajectory reveals that the SWCNT can effectively bind to the HIV-1-PR active site and regulate the flap dynamics such as maintaining the flap-flap closed. To gain an insight into the binding affinity, we also performed the MM-PBSA based binding free energy calculations for the four HIV-PR/SWCNT complexes. It was observed that, although the binding between the SWCNT and the HIV-PR decreases due to the mutations, the SWCNTs bind to the HIV-PRs 3-5 folds stronger than the most potent HIV-1-PR inhibitor, TMC114. Remarkably, the significant interactions with binding energy higher than 1kcal/mol focus on the flap and active regions, which favors closing flap-flap and deactivating the active residues of the HIV-PR. The flap dynamics and binding strength information for HIV-PR and SWCNTs can help design SWCNT-based HIV-1-PR inhibitors. PMID:23142620

  12. 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.

  13. Non-Hermitian tight-binding network engineering

    CERN Document Server

    Longhi, Stefano

    2016-01-01

    We suggest a simple method to engineer a tight-binding quantum network based on proper coupling to an auxiliary non-Hermitian cluster. In particular, it is shown that effective complex non-Hermitian hopping rates can be realized with only complex on-site energies in the network. Three applications of the Hamiltonian engineering method are presented: the synthesis of a nearly transparent defect in an Hermitian linear lattice; the realization of the Fano-Anderson model with complex coupling; and the synthesis of a $\\mathcal{PT}$-symmetric tight-binding lattice with a bound state in the continuum.

  14. 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.

  15. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase

    OpenAIRE

    Mondal, Jagannath; Friesner, Richard A.; Berne, B. J.

    2014-01-01

    Computer simulations are used to determine the free energy landscape for the binding of the anticancer drug Dasatinib to its src kinase receptor and show that before settling into a free energy basin the ligand must surmount a free energy barrier. An analysis based on using both the ligand-pocket separation and the pocket-water occupancy as reaction coordinates shows that the free energy barrier is a result of the free energy cost for almost complete desolvation of the binding pocket. The sim...

  16. 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...

  17. BINDING ISOTHERMS SURFACTANT-PROTEINS

    OpenAIRE

    Elena Irina Moater; Cristiana Radulescu; Ionica Ionita

    2011-01-01

    The interactions between surfactants and proteins shows some similarities with interactions between surfactants and polymers, but the hydrophobic amphoteric nature of proteins and their secondary and tertiary structure components make them different from conventional polymer systems. Many studies from the past about surfactant - proteins bonding used the dialysis techniques. Other techniques used to determine the binding isotherm, included ultrafiltration, ultracentrifugation, potentiometry, ...

  18. Cellulose binding domain fusion proteins

    Energy Technology Data Exchange (ETDEWEB)

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    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.

  19. Partitioning of metals in different binding phases of tropical estuarine sediments: importance of metal chemistry

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, P.; Chakraborty, S.; Vudamala, K.; Sarkar, Arindam; Nath, B.N.

    Distribution of metals in different binding phases of estuarine sediments provides chemically significant description of metal–sediment interactions. This study describes the influences of ligand field stabilization energy (LFSE), Jahn–Teller effect...

  20. 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.