Search results for "Binding"
showing 10 items of 3896 documents
Comparative theoretical study of the Ag–MgO (100) and (110) interfaces
1999
We have calculated the atomic and electronic structures of Ag–MgO(100) and (110) interfaces using a periodic (slab) model and an ab initio Hartree–Fock approach with a posteriori electron correlation corrections. The electronic structure information includes interatomic bond populations, effective charges, and multipole moments of ions. This information is analyzed in conjunction with the interface binding energy and the equilibrium distances for both interfaces for various coverages. There are significant differences between partly covered surfaces and surfaces with several layers of metal, and these can be understood in terms of electrostatics and the electron density changes. For complet…
The Greenland shark Somniosus microcephalus—Hemoglobins and ligand-binding properties
2017
A large amount of data is currently available on the adaptive mechanisms of polar bony fish hemoglobins, but structural information on those of cartilaginous species is scarce. This study presents the first characterisation of the hemoglobin system of one of the longest-living vertebrate species (392 +/- 120 years), the Arctic shark Somniosus microcephalus. Three major hemoglobins are found in its red blood cells and are made of two copies of the same a globin combined with two copies of three very similar beta subunits. The three hemoglobins show very similar oxygenation and carbonylation properties, which are unaffected by urea, a very important compound in marine elasmobranch physiology.…
Use of Density Functional Based Tight Binding Methods in Vibrational Circular Dichroism.
2018
Vibrational circular dichroism (VCD) is a spectroscopic technique used to resolve the absolute configuration of chiral systems. Obtaining a theoretical VCD spectrum requires computing atomic polar and axial tensors on top of the computationally demanding construction of the force constant matrix. In this study we evaluated a VCD model in which all necessary quantities are obtained with density functional based tight binding (DFTB) theory. The analyzed DFTB parametrizations fail at providing accurate vibrational frequencies and electric dipole gradients but yield reasonable normal modes at a fraction of the computational cost of density functional theory (DFT). Thus, by applying DFTB in comp…
Magnetic properties of exciton trapped by an off-center ionized donor in single quantum dot
2021
Abstract It is known that the lines of exciton (X) and exciton trapped by an ionized donor ( D + , X ) are often very close which makes very difficult their experimental identification. In order to facilitate their distinction in spherical quantum dots, we investigate the effect of an applied magnetic field studying the binding energy of the complex ( D + , X ) as function of dot size and the ionized donor position. Our calculation is using a variational approach taking into account the interactions between all charge carriers. Our results show that the complex is more sensitive to the magnetic field than the exciton and that the energy of the exciton is not sufficiently affected when the i…
Composition dependence ofSi1−xGexsputter yield
2005
Sputtering yields have been measured for unstrained ${\mathrm{Si}}_{1\ensuremath{-}x}{\mathrm{Ge}}_{x}$ $(x=0--1)$ alloys when bombarded with ${\mathrm{Ar}}^{+}$ ions within the linear cascade regime. Nonlinear S-shape dependence of the sputter yield as a function of the alloy composition has been revealed. The dependence is analyzed within the frameworks of the cascade theory conventionally accepted to be the most systematic to date theoretical approach in sputtering. In view of a linear composition dependence predicted for the sputter yield by the cascade theory adapted for polyatomic substrates, the nonlinearity observed in our experiments is shown to be related to the alloying effect on…
Theoretical investigation of the potential energy surface of the van der Waals complex CH4-N-2
2009
International audience; The interaction potential energy surface of the van der Waals CH4-N-2 complex has been calculated for a broad range of intermolecular separations and configurations in the approximation of rigid interacting molecules at the CCSD(T) and MP2 levels of theory using the correlation consistent aug-cc-pVTZ basis set. The BSSE correction was taken into account for all the calculations. The most stable configurations of the complex were found. Binding energies were calculated in the CBS limit with accounting for the molecular deformations. The harmonic and anharmonic fundamental vibrational frequencies and rotational constants for the ground and first excited vibrational sta…
MD Simulation Investigation on the Binding Process of Smoke-Derived Germination Stimulants to Its Receptor
2019
Karrikins (KARs) are a class of smoke-derived seed germination stimulants with great significance in both agriculture and plant biology. By means of direct binding to the receptor protein KAI2, the compounds can initiate the KAR signal transduction pathway, hence triggering germination of the dormant seeds in the soil. In the research, several molecular dynamics (MD) simulation techniques were properly integrated to investigate the binding process of KAR1 to KAI2 and reveal the details of the whole binding event. The calculated binding free energy, -7.00 kcal/mol, is in good agreement with the experimental measurement, -6.83 kcal/mol. The obtained PMF profile indicates the existence of thre…
Oxoanion binding to a cyclic pseudopeptide containing 1,4-disubstituted 1,2,3-triazole moieties
2016
A macrocyclic pseudopeptide 3 is described featuring three amide groups and three 1,4-disubstituted 1,2,3-triazole units along the ring. This pseudopeptide was designed such that the amide NH groups and the triazole CH groups converge toward the cavity, thus creating an environment well suited for anion recognition. Conformational studies in solution combined with X-ray crystallography confirmed this preorganisation. Solubility of 3 restricted binding studies to organic media such as 5 vol% DMSO/acetone or DMSO/water mixtures with a water content up to 5 vol%. These binding studies demonstrated that 3 binds to a variety of inorganic anions in DMSO/acetone including chloride, nitrate, sulfat…
Solution Conformation and Self‐Assembly of Ferrocenyl(thio)ureas
2016
Conformations and (dis)assembly processes of ureas and thioureas are of fundamental importance in supramolecular chemistry, anion binding, or crystal engineering, both in solution and in the solid state. For sensing and switching processes a redox-active unit, such as the ferrocene/ferrocenium couple, is especially suitable. Here, self-assembly processes of redox-active ferrocenyl(thio)ureas FcNHC(X)NHR [X = O, R = Fc (1), Ph (2), 1-naphthyl (3), Me (4), Et (5); X = S, R = Fc (6), 1-anthracenyl (7)] through hydrogen bonds – both in the solid state and in THF and CH2Cl2 solution – are reported. Special emphasis is placed on the impact of nonclassical intramolecular NH···Fe hydrogen bonds in …
Macrocyclic complexes based on [N⋯I⋯N]+ halogen bonds
2021
New 1–2 nm macrocyclic iodine(I) complexes prepared VIA a simple ligand exchange reaction manifest rigid 0.5–1 nm cavities that bind the hexafluorophosphate anion in the gas phase. The size of the cavities and the electrostatic interactions with the iodine(I) cations influence the anion binding properties of these macrocyclic complexes.