962 resultados para Density functional theory calculations
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Pós-graduação em Química - IQ
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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
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The abundance of alpha-fetoprotein (AFP), a natural protein produced by the fetal yolk sac during pregnancy, correlates with lower incidence of estrogen receptor positive (ER+) breast cancer. The pharmacophore region of AFP has been narrowed down to a four amino acid (AA) region in the third domain of the 591 AA peptide. Our computational study focuses on a 4-mer segment consisting of the amino acids threonine-proline-valine-asparagine (TPVN). We have run replica exchange molecular dynamics (REMD) simulations and used 120 configurational snapshots from the total trajectory as starting configurations for quantum chemical calculations. We optimized structures using semiempirical (PM3, PM6, PM6-D2, PM6-H2, PM6-DH+, PM6-DH2) and density functional methods (TPSS, PBE0, M06-2X). By comparing the accuracy of these methods against RI-MP2 benchmarks, we devised a protocol for calculating the lowest energy conformers of these peptides accurately and efficiently. This protocol screens out high-energy conformers using lower levels of theory and outlines a general method for predicting small peptide structures.
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An electronic phase with coexisting magnetic and ferroelectric order is predicted for graphene ribbons with zigzag edges. The electronic structure of the system is described with a mean-field Hubbard model that yields results very similar to those of density functional calculations. Without further approximations, the mean-field theory is recasted in terms of a BCS wave function for electron-hole pairs in the edge bands. The BCS coherence present in each spin channel is related to spin-resolved electric polarization. Although the total electric polarization vanishes, due to an internal phase locking of the BCS state, strong magnetoelectric effects are expected in this system. The formulation naturally accounts for the two gaps in the quasiparticle spectrun, Δ0 and Δ1, and relates them to the intraband and interband self-energies.
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We perform density functional calculations to investigate the structure of the intermetallic alloy FeRh under epitaxial strain. Bulk FeRh exhibits a metamagnetic transition from a low-temperature antiferromagnetic (AFM) phase to a ferromagnetic phase at 350 K, and its strain dependence is of interest for tuning the transition temperature to the room-temperature operating conditions of typical memory devices. We find an unusually strong dependence of the structural energetics on the choice of exchange-correlation functional, with the usual local density approximation yielding the wrong ground-state structure, and generalized gradient (GGA) extensions being in better agreement with the bulk experimental structure. Using the GGA we show the existence of a metastable face-centered-cubic-like AFM structure that is reached from the ground-state body-centered-cubic-like AFM structure by following the epitaxial Bain path. We show that the behavior is well described using nonlinear elasticity theory, which captures the softening and eventual sign change of the orthorhombic shear modulus under compressive strain, consistent with this structural instability. Finally, we predict the existence of an additional unit-cell-doubling lattice instability, which should be observable at low temperature.
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The present study measures the increase in serum carotenoid concentration in 30 healthy individuals after supplementation with a low dose xanthophyll ester (3 and 6 mg of lutein equivalent/per day) when compared to a placebo. Serum levels of carotenoids were measured using HPLC and showed an increase in the concentration of lutein, zeaxanthin and four lutein metabolites proportional to dose. In order to further assess the importance of the end-group structure in carotenoids we have investigated the influence of the end-group type and functionality on the conformational energy barrier. We used the density functional method implemented on GAUSSIAN 98 to calculate the conformational energy curves for rotation of the P-ring or the E-ring relative to short polyene chains around the C6-C7 single bond. A large barrier is observed for the interconversion of conformers in the E-rings (8 kcal/mol) when compared to beta rings (2.3-3 kcal/mol).
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First-principles electronic structure methods are used to find the rates of inelastic intravalley and intervalley n-type carrier scattering in Si1-xGex alloys. Scattering parameters for all relevant Delta and L intra- and intervalley scattering are calculated. The short-wavelength acoustic and the optical phonon modes in the alloy are computed using the random mass approximation, with interatomic forces calculated in the virtual crystal approximation using density functional perturbation theory. Optical phonon and intervalley scattering matrix elements are calculated from these modes of the disordered alloy. It is found that alloy disorder has only a small effect on the overall inelastic intervalley scattering rate at room temperature. Intravalley acoustic scattering rates are calculated within the deformation potential approximation. The acoustic deformation potentials are found directly and the range of validity of the deformation potential approximation verified in long-wavelength frozen phonon calculations. Details of the calculation of elastic alloy scattering rates presented in an earlier paper are also given. Elastic alloy disorder scattering is found to dominate over inelastic scattering, except for almost pure silicon (x approximate to 0) or almost pure germanium (x approximate to 1), where acoustic phonon scattering is predominant. The n-type carrier mobility, calculated from the total (elastic plus inelastic) scattering rate, using the Boltzmann transport equation in the relaxation time approximation, is in excellent agreement with experiments on bulk, unstrained alloys..
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This is the second in a series of articles whose ultimate goal is the evaluation of the matrix elements (MEs) of the U(2n) generators in a multishell spin-orbit basis. This extends the existing unitary group approach to spin-dependent configuration interaction (CI) and many-body perturbation theory calculations on molecules to systems where there is a natural partitioning of the electronic orbital space. As a necessary preliminary to obtaining the U(2n) generator MEs in a multishell spin-orbit basis, we must obtain a complete set of adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis. The zero-shift coefficients were obtained in the first article of the series. in this article, we evaluate the nonzero shift adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis. We then demonstrate that the one-shell versions of these coefficients may be obtained by taking the Gelfand-Tsetlin limit of the two-shell formulas. These coefficients,together with the zero-shift types, then enable us to write down formulas for the U(2n) generator matrix elements in a two-shell spin-orbit basis. Ultimately, the results of the series may be used to determine the many-electron density matrices for a partitioned system. (C) 1998 John Wiley & Sons, Inc.
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Flash vacuum thermolysis of quinolizinones is a new way of generating ketenes. The title ketene is obtained from 1-cyano-2-hydroxyquinolizine-4-one and characterized by its Ar matrix infrared spectrum. (C) Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany 2002.
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The synthesis of two new inherently chiral calix[4]arenes (ICCs, 1 and 2), endowed with electron-rich concave surfaces, has been achieved through the desymmetrization of a lower rim distal-bridged oxacyclophane (OCP) macrocycle. The new highly emissive ICCs were resolved by chiral HPLC, and the enantiomeric nature of the isolated antipodes proved by electronic circular dichroism (CD). Using time-dependent density functional calculations of CD spectra, their absolute configurations were established. NMR studies with (S)-Pirkle's alcohol unequivocally showed that the host-guest interactions occur in the chiral pocket comprehending the calix-OCP exo cavities and the carbazole moieties.
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[RuCl(arene)(-Cl)](2) dimers were treated in a 1:2 molar ratio with sodium or thallium salts of bis- and tris(pyrazolyl)borate ligands [Na(BpBr3)], [Tl(TpBr3)], and [Tl(Tp(iPr,4Br))]. Mononuclear neutral complexes [RuCl(arene)((2)-BpBr3)] (1: arene=p-cymene (cym); 2: arene=hexamethylbenzene (hmb); 3: arene=benzene (bz)), [RuCl(arene)((2)-TpBr3)] (4: arene=cym; 6: arene=bz), and [RuCl(arene)((2)-Tp(iPr,4Br))] (7: arene=cym, 8: arene=hmb, 9: arene=bz) have been always obtained with the exception of the ionic [Ru-2(hmb)(2)(-Cl)(3)][TpBr3] (5), which formed independently of the ratio of reactants and reaction conditions employed. The ionic [Ru(CH3OH)(cym)((2)-BpBr3)][X] (10: X=PF6, 12: X=O3SCF3) and the neutral [Ru(O2CCF3)(cym)((2)-BpBr3)] (11) have been obtained by a metathesis reaction with corresponding silver salts. All complexes 1-12 have been characterized by analytical and spectroscopic data (IR, ESI-MS, H-1 and (CNMR)-C-13 spectroscopy). The structures of the thallium and calcium derivatives of ligand TpBr3, [Tl(TpBr3)] and [Ca(dmso)(6)][TpBr3](2)2DMSO, of the complexes 1, 4, 5, 6, 11, and of the decomposition product [RuCl(cym)(Hpz(iPr,4Br))(2)][Cl] (7) have been confirmed by using single-crystal X-ray diffraction. Electrochemical studies showed that 1-9 and 11 undergo a single-electron (RuRuIII)-Ru-II oxidation at a potential, measured by cyclic voltammetry, which allows comparison of the electron-donor characters of the bis- and tris(pyrazol-1-yl)borate and arene ligands, and to estimate, for the first time, the values of the Lever E-L ligand parameter for BpBr3, TpBr3, and Tp(iPr,4Br). Theoretical calculations at the DFT level indicated that both oxidation and reduction of the Ru complexes under study are mostly metal-centered with some involvement of the chloride ligand in the former case, and also demonstrated that the experimental isolation of the (3)-binuclear complex 5 (instead of the mononuclear 5) is accounted for by the low thermodynamic stability of the latter species due to steric reasons.
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The average multipole surface-plasmon energy for simple metals, as well as that of ordinary surface and bulk plasmons, is obtained using energy-weighted moments of the electronic response to sufficiently general external perturbations. A local approximation of exchange and correlation effects is used within a jellium model. Band-structure effects are incorporated through an effective electronic mass. Taking advantage of the transparency of the method, we analyze under what circumstances such modes might be observable. It is shown that due to an interplay between Coulomb and kinetic energies, the multipole modes become unobservable for increasing values of the transferred momentum (q) parallel to the surface. The value of q at which the multipole mode becomes unobservable is much smaller than the cutoff value for Landau damping. The effect of the electronic surface diffuseness is also analyzed. We compare our results with previous density-functional calculations and with recent experimental data for Na, K, and Cs.
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Recent magnetotransport experiments of holes in InGaAs quantum dots [D. Reuter, P. Kailuweit, A. D. Wieck, U. Zeitler, O. Wibbelhoff, C. Meier, A. Lorke, and J. C. Maan, Phys. Rev. Lett. 94, 026808 (2005)] are interpreted by employing a multiband k¿p Hamiltonian, which considers the interaction between heavy hole and light hole subbands explicitly. No need of invoking an incomplete energy shell filling is required within this model. The crucial role we ascribe to the heavy hole-light hole interaction is further supported by one-band local-spin-density functional calculations, which show that Coulomb interactions do not induce any incomplete hole shell filling and therefore cannot account for the experimental magnetic field dispersion.
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We present static and dynamical properties of linear vortices in 4He droplets obtained from density functional calculations. By comparing the adsorption properties of different atomic impurities embedded in pure droplets and in droplets where a quantized vortex has been created, we suggest that Ca atoms should be the dopant of choice to detect vortices by means of spectroscopic experiments.
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The interaction of atomic F and Cl with Si4H9 and Ge4H9 cluster models has been studied by using ab initio pseudopotentials and basis sets of increasing complexity. The results show that the effect of d orbitals is important in order to reproduce the experimental findings. However, the use of polarization functions in the atoms which are directly involved in the chemisorption bond leads to results which are very close to those obtained using extended basis sets. The local nature of the chemisorption bond is also interpreted by means of a Mulliken population analysis. For F-Si4H9 and Cl-Si4H9 the present results are in good agreement with previous ab initio all-electron calculations, and for the chemisorption of Cl on Si(111) and Ge(111) surfaces, good agreement is found with respect to the available experimental results as well as with previous slab calculations based on the local-density-functional formalism.