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Author

A. B. F. da Silva

Other affiliations: Simon Fraser University
Bio: A. B. F. da Silva is an academic researcher from University of São Paulo. The author has contributed to research in topics: Gaussian & Hartree–Fock method. The author has an hindex of 24, co-authored 88 publications receiving 1632 citations. Previous affiliations of A. B. F. da Silva include Simon Fraser University.


Papers
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Journal ArticleDOI
TL;DR: In this paper, a universal Gaussian basis set was developed for relativistic Dirac-Fock calculations on atoms and molecules, and the Dirac Fock energies computed by using this single set of the universal GAussian basis for the atoms, He ([ital Z]=2) through No ([italZ]=102), were in excellent agreement with the corresponding numerical finite-difference DiracFock method.
Abstract: A universal Gaussian basis set is developed for accurate [ital ab] [ital initio] relativistic Dirac-Fock calculations on atoms and molecules. The Dirac-Fock energies computed by using this single set of the universal Gaussian basis for the atoms, He ([ital Z]=2) through No ([ital Z]=102), are in excellent agreement with the corresponding numerical finite-difference Dirac-Fock method. The total Dirac-Fock energies for lighter atoms agree with the corresponding numerical limit to a part in 10[sup 9] and for heavier systems to a part in 10[sup 8]. The total energy for the heaviest system, No ([ital Z]=102), calculated with our universal Gaussian basis set differs from the corresponding numerical limit by only 4 mhartrees.

151 citations

Journal ArticleDOI
TL;DR: A critical point of view on the main MLT shows their potential ability as a valuable tool in drug design and shows that MLT have significant advantages.
Abstract: The interest in the application of machine learning techniques (MLT) as drug design tools is growing in the last decades. The reason for this is related to the fact that the drug design is very complex and requires the use of hybrid techniques. A brief review of some MLT such as self-organizing maps, multilayer perceptron, bayesian neural networks, counter-propagation neural network and support vector machines is described in this paper. A comparison between the performance of the described methods and some classical statistical methods (such as partial least squares and multiple linear regression) shows that MLT have significant advantages. Nowadays, the number of studies in medicinal chemistry that employ these techniques has considerably increased, in particular the use of support vector machines. The state of the art and the future trends of MLT applications encompass the use of these techniques to construct more reliable QSAR models. The models obtained from MLT can be used in virtual screening studies as well as filters to develop/discovery new chemicals. An important challenge in the drug design field is the prediction of pharmacokinetic and toxicity properties, which can avoid failures in the clinical phases. Therefore, this review provides a critical point of view on the main MLT and shows their potential ability as a valuable tool in drug design.

138 citations

Journal ArticleDOI
TL;DR: In this paper, a universal Gaussian basis set is developed that leads to relativistic Dirac-Fock SCF energies of comparable accuracy as that obtained by the accurate numerical finite-difference method (GRASP2 package) [J. Phys. B 25, 1 (1992)].
Abstract: A universal Gaussian basis set is developed that leads to relativistic Dirac–Fock SCF energies of comparable accuracy as that obtained by the accurate numerical finite‐difference method (GRASP2 package) [J. Phys. B 25, 1 (1992)]. The Gaussian‐type functions of our universal basis set satisfy the relativistic boundary conditions associated with the finite nuclear model for a finite speed of light and conform to the so‐called kinetic balance at the nonrelativistic limit. We attribute the exceptionally high accuracy obtained in our calculations to the fact that the representation of the relativistic dynamics of an electron in a spherical ball finite nucleus near the origin in terms of our universal Gaussian basis set is as accurate as that provided by the numerical finite‐difference method. Results of the Dirac–Fock–Coulomb energies for a number of atoms up to No (Z=102) and some negative ions are presented and compared with the recent results obtained with the numerical finite‐difference method and geometrical Gaussian basis sets by Parpia, Mohanty, and Clementi [J. Phys. B 25, 1 (1992)]. The accuracy of our calculations is estimated to be within a few parts in 109 for all the atomic systems studied.

74 citations

Journal ArticleDOI
TL;DR: In this article, the solvent effects in the structure and electronic spectra of some cationic dyes: acridine orange, proflavine, safranine, neutral red, thionine and methylene blue were studied.
Abstract: We present a quantum-mechanical study on the solvent effects in the structure and electronic spectra of some cationic dyes: acridine orange, proflavine, safranine, neutral red, thionine and methylene blue. The geometry optimizations were carried out with the AM1 and DFT (with B3LYP functional) methods and the theoretical spectra of the dyes under study were obtained with Zindo time-dependent methods (TD–DFT and TD–HF). The solvation methodology adopted was the integral equation formulation (IEF) version of the polarizable continuum model (PCM).

68 citations

Journal ArticleDOI
TL;DR: In this paper, AM1 calculations for the EHOMO and ELUMO of 15 biomolecules are performed with the aim to obtain a scale for the electron-donating and electron-accepting character of biom molecules, as they can interact in the biological environment through a charge-transfer mechanism.
Abstract: Energy of the highest occupied molecular orbital (EHOMO) and energy of the lowest unoccupied molecular orbital (ELUMO) are very often related to the electron-donating (EHOMO) and electron-accepting (ELUMO) character of a molecule. In this work AM1 calculations for the EHOMO and ELUMO of 15 biomolecules are performed with the aim to obtain a scale for the electron-donating and electron-accepting character of biomolecules, as they can interact in the biological environment through a charge-transfer mechanism. From the EHOMO and ELUMO values obtained with the AM1 semiempirical method, we were able to classify the 15 compounds studied into four groups: A (good electron-donor molecules), B (good electron-acceptor molecules), C (moderate electron-donor molecules), and D (compounds that behave as both electron-donor and electron-acceptor molecules). © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 95: 126–132, 2003

62 citations


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Proceedings Article
14 Jul 1996
TL;DR: The striking signature of Bose condensation was the sudden appearance of a bimodal velocity distribution below the critical temperature of ~2µK.
Abstract: Bose-Einstein condensation (BEC) has been observed in a dilute gas of sodium atoms. A Bose-Einstein condensate consists of a macroscopic population of the ground state of the system, and is a coherent state of matter. In an ideal gas, this phase transition is purely quantum-statistical. The study of BEC in weakly interacting systems which can be controlled and observed with precision holds the promise of revealing new macroscopic quantum phenomena that can be understood from first principles.

3,530 citations

Journal ArticleDOI
TL;DR: In this article, a medium basis set based upon contractions of Gaussian primitives was developed for the third-row elements K through Zn. The basis functions generalize the 6-31G and 631G* sets commonly used for atoms up to Ar.
Abstract: Medium basis sets based upon contractions of Gaussian primitives are developed for the third-row elements K through Zn. The basis functions generalize the 6-31G and 6-31G* sets commonly used for atoms up to Ar. They use six primitive Gaussians for 1s, 2s, 2p, 3s, and 3p orbitals, and a split-valence pair of three and one primitives for valence orbitals, which are 4s and 5p for atoms K and Ca, and 4s, 4p, and 3d for atoms Sc through Zn. A 6-31G* set is formed by adding a single set of Gaussian polarization functions to the 6-31G set. They are Cartesian d-functions for atoms K and Ca, and Cartesian f-functions for atoms Sc through Zn. Comparison with experimental data shows relatively good agreement with bond lengths and angles for representative vapor-phase metal complexes.

1,709 citations

Journal ArticleDOI
TL;DR: HSE is a fast and accurate alternative to established density functionals, especially for solid state calculations, and correctly predicts semiconducting behavior in systems where pure functionals erroneously predict a metal, such as, for instance, Ge.
Abstract: This work assesses the Heyd-Scuseria-Ernzerhof (HSE) screened Coulomb hybrid density functional for the prediction of lattice constants and band gaps using a set of 40 simple and binary semiconductors. An extensive analysis of both basis set and relativistic effects is given. Results are compared with established pure density functionals. For lattice constants, HSE outperforms local spin-density approximation (LSDA) with a mean absolute error (MAE) of 0.037 A for HSE vs 0.047 A for LSDA. For this specific test set, all pure functionals tested produce MAEs for band gaps of 1.0–1.3 eV, consistent with the very well-known fact that pure functionals severely underestimate this property. On the other hand, HSE yields a MAE smaller than 0.3 eV. Importantly, HSE correctly predicts semiconducting behavior in systems where pure functionals erroneously predict a metal, such as, for instance, Ge. The short-range nature of the exchange integrals involved in HSE calculations makes their computation notably faster than regular hybrid functionals. The current results, paired with earlier work, suggest that HSE is a fast and accurate alternative to established density functionals, especially for solid state calculations.

1,564 citations