Dimensional Compactification and Two-Particle Binding

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Binding and structure of tetramers in the scaling limit

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Photoreflectance studies of optical transitions in cubic GaN grown on GaAs(001) substrates

The optical properties of cubic GaN epitaxial layers were investigated by modulated photoreflectance (PR) and photoluminescence in the temperature interval from 5 to 300 K. The epilayers were grown on GaAs(001) substrates by molecular beam epitaxy using a nitrogen RIF-activated plasma source. The PR spectra show a transition which is well fitted using the third-derivative functional form of the unperturbed dielectric function, which we interpret as band-to-band transition. Our results allow determination of the temperature dependence of the main gap of c-GaN and give insights into the residual strain in the film, as well as allow us to estimate the binding energy of the complex formed by an exciton bound to a neutral acceptor. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Low-energy correlations in the positronium-hydrogen-atom system

Employing a nonlocal model potential for electron exchange we study positronium-hydrogen-atom (Ps-H) scattering using a five-state coupled-channel model allowing for Ps(2s,2p)H(1s) and Ps(1s)H(2s,2p) excitations. We find remarkable correlations among S-wave Ps-H binding energy, scattering length, effective range, and resonance energy in the electronic singlet state. Using these correlations we predict fairly accurate values of singlet Ps-H scattering length (3.50a0) and effective range (1.65a0).

Interaction of Bacillus thuringiensis Cry1 and Vip3A proteins with Spodoptera frugiperda midgut binding sites

Vip3Aa, Vip3Af, Cry1Ab, and Cry1Fa were tested for their toxicities and binding interactions. Vip3A proteins were more toxic than Cry1 proteins. Binding assays showed independent specific binding sites for Cry1 and Vip3A proteins. Cry1Ab and Cry1Fa competed for the same binding sites, whereas Vip3Aa competed for those of Vip3Af. Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Search for new physics in final states with a lepton and missing transverse energy in pp collisions at the LHC

This Letter describes the search for an enhanced production rate of events with a charged lepton and a neutrino in high-energy pp collisions at the LHC. The analysis uses data collected with the CMS detector, with an integrated luminosity of 5.0 fb-1 at √s=7 TeV, and a further 3.7 fb -1 at √s=8 TeV. No evidence is found for an excess. The results are interpreted in terms of limits on a heavy charged gauge boson (W ′) in the sequential standard model, a split universal extra dimension model, and contact interactions in the helicity-nonconserving model. For the last, values of the binding energy below 10.5 (8.8) TeV in the electron (muon) channel are excluded at a 95% confidence level. Interpreting the ℓν final state in terms of a heavy W′ with standard model couplings, masses below 2.90 TeV are excluded. © 2013 CERN.

Theoretical prevision for the low-energy 3S1-3D1 mixing parameters

Using a recent shape-independent approximation for the 3S1-3D1 mixing parameter, theoretical prevision for the low-energy mixing parameters is made. The present prevision is consistent with the deuteron binding energy, its asymptotic D-state to S-state ratio, ηd, the triplet-scattering length, and the meson exchange tail of the tensor nucleon-nucleon potential. The theoretical prevision up to an incident laboratory energy of 25 MeV is consistent with the recent multi-energy determination of mixing parameters, but is much higher than many single-energy determinations of the same. The low single-energy values of the mixing parameter could be reproduced by meson-theoretical potentials only with a substantially reduced ηd. © 1994 The American Physical Society.

Metal binding selectivity of oxa-aza macrocyclic ligand: a DFT study of first- and second-row transition metal for four coordination systems

A detailed theoretical study of the 1,7,1l,17-tetraoxa-2,6,12,16-tetraaza-cycloeicosane ligand ([20]AneN(4)O(4)) coordinated to Fe2+, Co2+, Ni2+, Ru2+, Rh2+, and Pd2+ transition metal ions was carried out with the B3LYP method. Two different cases were performed: when nitrogen is the donor atom (1a (q) ) and also with the oxygen as the donor atom (1b (q) ). For all the cases performed in this study 1a (q) structures were always more stable than the 1b (q) ones. Considering each row is possible to see that the energy increases with the increase of the atomic number. The M2+ cation binding energies for the 1a (q) complexes increase with the following order: Fe2+ < Ru2+ < Co2+ < Ni2+ < Rh2+ < Pd2+.

Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections

For (H2O)n where n = 1–10, we used a scheme combining molecular dynamics sampling with high level ab initio calculations to locate the global and many low lying local minima for each cluster. For each isomer, we extrapolated the RI-MP2 energies to their complete basis set limit, included a CCSD(T) correction using a smaller basis set and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled and unscaled harmonic vibrational frequencies. The vibrational scaling factors were determined specifically for water clusters by comparing harmonic frequencies with VPT2 fundamental frequencies. We find the CCSD(T) correction to the RI-MP2 binding energy to be small (<1%) but still important in determining accurate conformational energies. Anharmonic corrections are found to be non-negligble; they do not alter the energetic ordering of isomers, but they do lower the free energies of formation of the water clusters by as much as 4 kcal/mol at 298.15 K.

Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections

For (H2O)n where n = 1–10, we used a scheme combining molecular dynamics sampling with high level ab initio calculations to locate the global and many low lying local minima for each cluster. For each isomer, we extrapolated the RI-MP2 energies to their complete basis set limit, included a CCSD(T) correction using a smaller basis set and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled and unscaled harmonic vibrational frequencies. The vibrational scaling factors were determined specifically for water clusters by comparing harmonic frequencies with VPT2 fundamental frequencies. We find the CCSD(T) correction to the RI-MP2 binding energy to be small (

Self-consistent relativistic band structure of the CH3NH3PbI3 perovskite

The electronic structure and properties of the orthorhombic phase of the CH 3 NH 3 PbI 3 perovskite are computed with density functional theory. The structure, optimized using a van der Waals functional, reproduces closely the unit cell volume. The experimental band gap is reproduced accurately by combining spin-orbit effects and a hybrid functional in which the fraction of exact exchange is tuned self-consistently to the optical dielectric constant. Including spin-orbit coupling strongly reduces the anisotropy of the effective mass tensor, predicting a low electron effective mass in all crystal directions. The computed binding energy of the unrelaxed exciton agrees with experimental data, and the values found imply a fast exciton dissociation at ambient temperature. Also polaron masses for the separated carriers are estimated. The values of all these parameters agree with recent indications that fast dynamics and large carrier diffusion lengths are key in the high photovoltaic efficiencies shown by these materials.

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

The search for novel leads is a critical step in the drug discovery process. Computational approaches to identify new lead molecules have focused on discovering complete ligands by evaluating the binding affinity of a large number of candidates, a task of considerable complexity. A new computational method is introduced in this work based on the premise that the primary molecular recognition event in the protein binding site may be accomplished by small core fragments that serve as molecular anchors, providing a structurally stable platform that can be subsequently tailored into complete ligands. To fulfill its role, we show that an effective molecular anchor must meet both the thermodynamic requirement of relative energetic stability of a single binding mode and its consistent kinetic accessibility, which may be measured by the structural consensus of multiple docking simulations. From a large number of candidates, this technique is able to identify known core fragments responsible for primary recognition by the FK506 binding protein (FKBP-12), along with a diverse repertoire of novel molecular cores. By contrast, absolute energetic criteria for selecting molecular anchors are found to be promiscuous. A relationship between a minimum frustration principle of binding energy landscapes and receptor-specific molecular anchors in their role as "recognition nuclei" is established, thereby unraveling a mechanism of lead discovery and providing a practical route to receptor-biased computational combinatorial chemistry.

A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding.

We propose a general mean field model of ligand-protein interactions to determine the thermodynamic equilibrium of a system at finite temperature. The method is employed in structural assessments of two human immuno-deficiency virus type 1 protease complexes where the gross effects of protein flexibility are incorporated by utilizing a data base of crystal structures. Analysis of the energy spectra for these complexes has revealed that structural and thermo-dynamic aspects of molecular recognition can be rationalized on the basis of the extent of frustration in the binding energy landscape. In particular, the relationship between receptor-specific binding of these ligands to human immunodeficiency virus type 1 protease and a minimal frustration principle is analyzed.

Promotion of purine nucleotide binding to thymidylate synthase by a potent folate analogue inhibitor, 1843U89.

A folate analogue, 1843U89 (U89), with potential as a chemotherapeutic agent due to its potent and specific inhibition of thymidylate synthase (TS; EC 2.1.1.45), greatly enhances not only the binding of 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUMP) and dUMP to Escherichia coli TS but also that of dGMP, GMP, dIMP, and IMP. Guanine nucleotide binding was first detected by CD analysis, which revealed a unique spectrum for the TS-dGMP-U89 ternary complex. The quantitative binding of dGMP relative to GMP, FdUMP, and dUMP was determined in the presence and absence of U89 by ultrafiltration analysis, which revealed that although the binding of GMP and dGMP could not be detected in the absence of U89 both were bound in its presence. The Kd for dGMP was about the same as that for dUMP and FdUMP, with binding of the latter two nucleotides being increased by two orders of magnitude by U89. An explanation for the binding of dGMP was provided by x-ray diffraction studies that revealed an extensive stacking interaction between the guanine of dGMP and the benzoquinazoline ring of U89 and hydrogen bonds similar to those involved in dUMP binding. In addition, binding energy was provided through a water molecule that formed hydrogen bonds to both N7 of dGMP and the hydroxyl of Tyr-94. Accommodation of the larger dGMP molecule was accomplished through a distortion of the active site and a shift of the deoxyribose moiety to a new position. These rearrangements also enabled the binding of GMP to occur by creating a pocket for the ribose 2' hydroxyl group, overcoming the normal TS discrimination against nucleotides containing the 2' hydroxyl.

Effect of dipole polarizability on positron binding by strongly polar molecules

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 the polarization potential via perturbation theory and non-perturbatively. The perturbative model makes reliable predictions of binding energies for a range of polar organic molecules and hydrogen cyanide. The model also agrees with 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). The effective core radii, however, remain unphysically small for most molecules. Treating molecular polarization non-perturbatively leads to physically meaningful core radii for all of the molecules studied and enables even more accurate predictions of binding energies to be made for nearly all of the molecules considered.