E. W. S. Caetano

Structural and optoelectronic properties, and infrared spectrum of cubic BaSnO3 from first principles calculations

The electronic band structure, density of states, dielectric function, optical absorption, and infrared spectrum of cubic BaSnO3 were simulated using density functional theory, within both the local density and generalized gradient approximations, LDA and GGA, respectively. Dielectric optical permittivities and polarizabilities at ω=0 and ω=∞ were also estimated. Indirect band gaps E(R→Γ) of 1.01 eV (LDA) and 0.74 eV (GGA) were found, which are smaller than the experimental one (≈3.1 eV). A comparison of the calculated cubic BaSnO3 band gap with those of others stannates ASnO3 (A = Ca, Sr, Cd) already published highlights their dependence on each crystal profile. The cubic BaSnO3 effective masses of electrons and holes were computed by parabolic fittings along different directions at the conduction band minimum and valence band maximum, being anisotropic for both electrons and holes. The experimental band gap and calculated effective masses confirm the semiconductor character of cubic BaSnO3. Finally, the...

Electronic and optical properties of CaCO3 calcite, and excitons in Si@CaCO3 and CaCO3@SiO2 core-shell quantum dots

Density functional theory calculations of the electronic and optical properties of the CaCO3 calcite polymorph were performed within both the local density (LDA) and generalized gradient (GGA) approximations, respectively. The carriers effective masses are estimated, and the energy gap is shown to be indirect, with and (for comparison, the experimental value is 6.0 ? 0.35?eV). Two optical absorption regimes are predicted, and the dielectric function does not change considerably with the light polarization. The confinement features of excitons in Si@CaCO3 and CaCO3@SiO2 spherical core-shell quantum dots are also presented.

Adsorption of Ascorbic Acid on the C60 Fullerene

Adsorption of ascorbic acid (AsA) on C60 is investigated using classical molecular mechanics and density functional theory (DFT). Classical annealing was performed to explore the space of molecular configurations of ascorbic acid adsorbed on C60, searching for optimal geometries. From the structure with the smallest total energy, 10 initial configurations were prepared by applying rotations of 90 degrees about three orthogonal axes. Each one of these configurations was optimized using DFT (for both LDA and GGA exchange-correlation functionals), and an estimate of their total and adsorption energies was found. Different configurations have minimal adsorption energies (defined here as the total energy of the adsorbate minus the total energy of the separate molecules) from -0.54 to -0.10 eV, with distinct optimal distances between the AsA and C60 centers of mass. According to a Hirshfeld population analysis, AsA is, in general, an acceptor of electrons from C60. Our results demonstrate the feasibility of noncovalent functionalization of C60 with AsA and provide minimal energy values for the several different configurations investigated. These results should be considered in reactions as a possible way to prevent against the oxidative damage and toxicity of C60. The beneficial effects of using AsA-C60 includes its action when administered together with levodopa, against the neurotoxicity generated by levodopa isolated, which opens new strategies for the Parkinsons disease treatment.

Quantum molecular modelling of ibuprofen bound to human serum albumin

The binding of the nonsteroidal anti-inflammatory drug ibuprofen (IBU) to human serum albumin (HSA) is investigated using density functional theory (DFT) calculations within a fragmentation strategy. Crystallographic data for the IBU–HSA supramolecular complex shows that the ligand is confined to a large cavity at the subdomain IIIA and at the interface between the subdomains IIA and IIB, whose binding sites are FA3/FA4 and FA6, respectively. The interaction energy between the IBU molecule and each amino acid residue of these HSA binding pockets was calculated using the Molecular Fractionation with Conjugate Caps (MFCC) approach employing a dispersion corrected exchange–correlation functional. Our investigation shows that the total interaction energy of IBU bound to HSA at binding sites of the fatty acids FA3/FA4 (FA6) converges only for a pocket radius of at least 8.5 A, mainly due to the action of residues Arg410, Lys414 and Ser489 (Lys351, Ser480 and Leu481) and residues in non-hydrophobic domains, namely Ile388, Phe395, Phe403, Leu407, Leu430, Val433, and Leu453 (Phe206, Ala210, Ala213, and Leu327), which is unusual. Our simulations are valuable for a better understanding of the binding mechanism of IBU to albumin and can lead to the rational design and the development of novel IBU-derived drugs with improved potency.

Antipsychotic Haloperidol Binding to the Human Dopamine D3 Receptor: Beyond Docking Through QM/MM Refinement Toward the Design of Improved Schizophrenia Medicines

As the dopamine D3R receptor is a promising target for schizophrenia treatment, an improved understanding of the binding of existing antipsychotics to this receptor is crucial for the development of new potent and more selective therapeutic agents. In this work, we have used X-ray cocrystallization data of the antagonist eticlopride bound to D3R as a template to predict, through docking essays, the placement of the typical antipsychotic drug haloperidol at the D3R receptor binding site. Afterward, classical and quantum mechanics/molecular mechanics (QM/MM) computations were employed to improve the quality of the docking calculations, with the QM part of the simulations being accomplished by using the density functional theory (DFT) formalism. After docking, the calculated QM improved total interaction energy EQMDI = -170.1 kcal/mol was larger (in absolute value) than that obtained with classical molecular mechanics improved (ECLDI = -156.3 kcal/mol) and crude docking (ECRDI = -137.6 kcal/mol) procedures. The QM/MM computations reveal the pivotal role of the Asp110 amino acid residue in the D3R haloperidol binding, followed by Tyr365, Phe345, Ile183, Phe346, Tyr373, and Cys114. Besides, it highlights the relevance of the haloperidol hydroxyl group axial orientation, which interacts with the Tyr365 and Thr369 residues, enhancing its binding to dopamine receptors. Finally, our computations indicate that functional substitutions in the 4-clorophenyl and in the 4-hydroxypiperidin-1-yl fragments (such as C3H and C12H hydrogen replacement by OH or COOH) can lead to haloperidol derivatives with distinct dopamine antagonism profiles. The results of our work are a first step using in silico quantum biochemical design as means to impact the discovery of new medicines to treat schizophrenia.

Structural, electronic and optical properties of ilmenite and perovskite CdSnO3 from DFT calculations

CdSnO(3) ilmenite and perovskite crystals were investigated using both the local density and generalized gradient approximations, LDA and GGA, respectively, of the density functional theory (DFT). The electronic band structures, densities of states, dielectric functions, optical absorption and reflectivity spectra related to electronic transitions were obtained, as well as the infrared absorption spectra after computing the vibrational modes of the crystals at q = 0. Dielectric optical permittivities and polarizabilities at ω = 0 and ∞ were also calculated. The results show that GGA-optimized geometries are more accurate than LDA ones, and the Kohn-Sham band structures obtained for the CdSnO(3) polymorphs confirm that ilmenite has an indirect band gap, while perovskite has a direct band gap, both being semiconductors. Effective masses for both crystals are obtained for the first time, being highly isotropic for electrons and anisotropic for holes. The optical properties reveal a very small degree of anisotropy of both crystals with respect to different polarization planes of incident light. The phonon calculation at q = 0 for perovskite CdSnO(3) does not show any imaginary frequencies, in contrast to a previous report suggesting the existence of a more stable crystal of perovskite CdSnO(3) with ferroelectric properties.

Triclinic CdSiO3 structural, electronic, and optical properties from first principles calculations

Quantum ab initio simulations were carried out to study the CdSiO3 triclinic crystal. Unit cell parameters and atomic positions were optimized to find a minimum total energy within the density functional theory (DFT) formalism in both the local density and generalized gradient approximations, LDA and GGA, respectively. Analysis of the Kohn?Sham electronic band structure shows that there are two very close indirect band gaps Eg(Z ? ?) = 2.57?eV (2.79?eV) and Eg(Q ? ?) = 2.59?eV (2.81?eV) for the GGA-PBE (LDA-CAPZ) computations, and a direct band gap Eg(? ? ?) = 2.57, 2.63?eV (2.85?eV). Effective masses for holes and electrons were estimated by parabolic fitting along different directions at the valence band maximum and conduction band minimum, and they are very anisotropic. A comparison with previously reported data for triclinic CaSiO3 (wollastonite) using the LDA-CAPZ exchange-correlation functional reveals that the substitution of calcium by cadmium changes the localization of the valence band maximum in reciprocal space and decreases the band gap energies. Optical properties (dielectric function, optical absorption) for incident light polarized along different crystalline planes were computed, the optical absorption for incident light with polarization along the 0?1?0 crystalline plane being the smallest for energies near the main band gap due to the spatial disposition of the SiO4 tetrahedra and CdO6 octahedra chains that build up the structure of triclinic CdSiO3.

Structural and optical properties of CaO

CaO is a wide band gap material yet unexplored for optoelectronics, but which was recently proposed as a candidate for spintronics applications. In the present work we report the results of an ab initio electronic band structure calculation of cubic CaO using both the local-density and the generalized gradient approximations. We performed the structural CaO crystal optimization, and calculated its optical properties, which are compared with the available experimental data and with other theoretical results for the cubic CaO structure.

Inactivation of ovine cyclooxygenase-1 by bromoaspirin and aspirin: a quantum chemistry description.

The resulting noncovalent bonding of the salicylic acid to ovine COX-1 after bromoaspirin and aspirin acetylation by Ser530 is investigated within the scope of density functional theory considering a 6.5 Å radius binding pocket. We have not only took full advantage of published X-ray structural data for the ovine COX-1 cocrystallized with bromoaspirin, but we also have improved that data through computation, finding good estimates for the hydrogen atom positions at the residues of the binding pocket, and repositioning the Ser530Ac[Br;H] lateral chain and salicylic acid by total energy minimization procedures employing LDA and GGA+D exchange-correlation functionals. Using bromoaspirin as a template, we have simulated the positioning of aspirin in the binding pocket, estimating its interaction energy with each of its neighbor COX-1 residues. We demonstrate that the binding energies of bromoaspirin and aspirin to COX-1 are very close when second-order quantum refinements of the structural data are performed, which points to an explanation on why the IC(50) values for the 126 μM COX-1 activity of both bromoaspirin and aspirin are practically the same. Attracting and repelling residues were identified, being shown that Arg120 is the most effective residue attracting the salicylic acid, followed by Ala527, Leu531, Leu359, and Ser353. On the other hand, Glu524 was found the most effective repulsive residue (strength interaction comparable to Arg120).

Molecular Signature in the Photoluminescence of α‐Glycine, L‐Alanine and L‐Asparagine Crystals: Detection, ab initio Calculations, and Bio‐sensor Applications

We present the photoluminescence spectra of α‐glycine, L‐alanine, and L‐asparagine crystals. They are broad and structured, comprising green to ultraviolet emission in the 1.75–3.60 eV range. Absorption measurements show that the band gap energies of the crystals are of the order of 5.0 eV. Ab initio calculations of their electronic structures allow for the assignment of the observed peaks in the visible region to lattice‐related processes of exciton nature associated with polaron levels. The very thin photoluminescence peaks in the ultraviolet region are assigned to intramolecular transitions, being a signature of the weakly interacting amino acid molecules in the crystals.