Search results for "Binding energy"
showing 10 items of 248 documents
Entropy–enthalpy compensation at the single protein level: pH sensing in the bacterial channel OmpF
2014
The pH sensing mechanism of the OmpF channel operates via ligand modification: increasing acidity induces the replacement of cations with protons in critical binding sites decreasing the channel conductance. Aside from the change in enthalpy associated with the binding, there is also a change in the microscopic arrangements of ligands, receptors and the surrounding solvent. We show that the pH-modulation of the single channel conduction involves small free energy changes because large enthalpic and entropic contributions change in opposite ways, demonstrating an approximate enthalpy–entropy compensation for different salts and concentrations. We wish to acknowledge the support from the Span…
Influence of electronic and geometric properties on melting of sodium clusters
2004
Systematics of the melting transition for sodium clusters with 40-355 atoms has been studied with both ab initio and semiclassical molecular dynamics simulations. The melting temperatures obtained with an ab initio method for Na55 + and Na93 + correlate well with the experimental results. The semiclassically determined melting temperatures show similarities with the experimentally determined ones in the size region from 55 to 93 and near size 142, and the latent heat in the size region from 55 to 139, but not elsewhere in the size region studied. This indicates that the nonmonotonical melting behavior observed experimentally cannot be fully explained by geometrical effects. The semiclassica…
Suitability ofMMGBSAfor the selection of correct ligand binding modes from docking results
2018
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics-generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…
Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues.
2007
Abstract Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. S-1360 is a potent and selective inhibitor of HIV-1 IN. In this work, we have carried out molecular dynamics (MD) simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach, to determine the protein–ligand interaction energy for S-1360 and two analogues. Analysis of the MD trajectories reveals that the strongest protein–inhibitor interactions, observed in the three studied complexes, are established with Lys-159 residue and Mg 2+ cation. Calculations of binding energy using BLYP/MM level of theory reveal that there is a direct rela…
Morphology and Band Structure of Orthorhombic PbS Nanoplatelets: An Indirect Band Gap Material
2021
PbS quantum dots and nanoplatelets (NPLs) are of enormous interest in the development of optoelectronic devices. However, some important aspects of their nature remain unclear. Recent studies have revealed that colloidal PbS NPLs may depart from the rock-salt crystal structure of bulk and form an orthorhombic (Pnma) modification instead. To gain insight into the implications of such a change over the optoelectronic properties, we have synthesized orthorhombic PbS NPLs and determined the lattice parameters by means of selected area electron diffraction measurements. We have then calculated the associated band structure using density functional theory with Perdew–Burke–Ernzerhof functional fo…
Low-temperature exciton absorption in InSe under pressure.
1992
We have investigated the effect of pressure on the lowest direct band-edge exciton of the layered semiconductor InSe by optical-absorption measurements at 10 K and for pressures up to 4 GPa. The Elliott-Toyozawa formalism is used to analyze the line shape of the exciton absorption spectra. In this way we determine the pressure dependence of the lowest direct band gap, the exciton binding energy, and the exciton linewidth. The band gap exhibits a pronounced nonlinear shift with pressure, which is a consequence of the strong anisotropy of intralayer and interlayer bonding. The exciton binding energy decreases with pressure, mainly due to the large increase of the low-frequency dielectric cons…
Dynamics of exciton creation and decay processes in composition – disordered InGaN thin films
2011
In the GaN-based ternary alloys, InGaN crystals have been recognized as key materials for e-h plasmas-exciton dynamics, because of large exciton binding energies (24.8 meV in GaN). We report investigations of creating and recombination dynamics of excitons in commercially important InxGa1-xN composition range from x = 0.1 to 0.18 in which nanoscale indium composition fluctuation occurs and formation of indium rich clusters acting as quantum dots (QD) can be expected. Three MOCVD grown samples having x = 0.1; 0.14 and 0.18 have been investigated using 3D picosecond transient PL spectroscopy. It has been found that the band to band photo excitation at 15 K in whole composition range results i…
MP2 Study of Physisorption of Molecular Hydrogen onto Defective Nanotubes: Cooperative Effect in Stone–Wales Defects
2016
We use large-scale MP2 calculations to investigate the physisorption of molecular hydrogen on (9,0) defective carbon nanotubes (CNTs) of C72H18. These large (supra)molecular systems are typically studied using conventional DFT methods, which do not describe well the van der Waals interactions responsible for this process. Here we use CCSD(T)-calibrated MP2 calculations to estimate binding energies by considering four defective structures (hydrogenated divacancy, octagon-pentagon, and two Stone-Wales defects). The largest physisorption energies for the nondefective CNT are for configurations in which H2 points toward the center of one ring. The computed interaction energies for defect-free C…
Precision mass measurements of neutron-rich nuclei between N=50 and 82
2012
Our knowledge of binding energies of neutron-rich nuclei has experienced a major revision during the last five years due to the introduction of Penning-trap based mass measurements. New mass values for nearly 300 nuclides produced in fission with uncertainties of 10 keV or less have become available. The data produced at three Penning trap facilities at Jyvaskyla, CERN-ISOLDE and Argonne cover all isotopic chains from Ni to Pr, except iodine. In this talk some of this data is reviewed and applied using the mass differentials such as two-neutron binding energy and odd-even staggering to probe their sensitivity on changes in nuclear structure and on the strength of the N=82 shell gap and asso…
Asymptotic normalization coefficients and continuum coupling in mirror nuclei
2012
Background: An asymptotic normalization coefficient (ANC) characterizes the asymptotic form of a one-nucleon overlap integral required for description of nucleon-removal reactions. Purpose: We investigate the impact of the particle continuum on proton and neutron ANCs for mirror systems from $p$- and $sd$-shell regions. Method: We use the real-energy and complex-energy continuum shell model approaches. Results: We studied the general structure of the single-particle ANCs as a function of the binding energy and orbital angular momentum. We computed ANCs in mirror nuclei for different physical situations, including capture reactions to weakly-bound and unbound states. Conclusions: We demonstr…