On polarization functions for Gaussian basis sets.

In this work, we introduce a technique to choose polarization functions directly from the primitive set of Gaussian exponent without the necessity to optimize or even reoptimized them. For this purpose, initially, we employed Gaussian basis sets generated by using the Polynomial Generator Coordinate Hartree-Fock (PGCHF) method, and later we extended our technique to the cc-pVQZ and pc-3 Gaussian basis sets in order to show how our technique works and how good it is. Using the new polarized basis sets, from our technique, total electronic energies, equilibrium geometries, and vibrational frequencies were calculated for a set of molecules containing atoms from H(Z = 1) to Ba(Z = 56).

Relativistic Prolapse-Free Gaussian Basis Sets of Quadruple-ζ Quality: (aug-)RPF-4Z. III. The f-Block Elements.

The f-block elements are addressed in this third part of a series of prolapse-free basis sets of quadruple-ζ quality (RPF-4Z). Relativistic adapted Gaussian basis sets (RAGBSs) are used as primitive sets of functions while correlating/polarization (C/P) functions are chosen by analyzing energy lowerings upon basis set increments in Dirac-Coulomb multireference configuration interaction calculations with single and double excitations of the valence spinors. These function exponents are obtained by applying the RAGBS parameters in a polynomial expression.

Relativistic Prolapse-Free Gaussian Basis Set of Quadruple-ζ Quality: (aug-)RPF-4Z. II. The d-Block Elements.

A series of relativistic prolapse-free Gaussian basis sets of quadruple-ζ quality has been developed: (aug-)RPF-4Z. Here, we report the (aug-)RPF-4Z sets for all the d-block elements (Sc-Cn). Molecular calculations at the Coupled Cluster level showed a significant reduction in computational demand in comparison with other well-known relativistic quadruple-ζ sets.

Relativistic Prolapse-Free Gaussian Basis Set of Quadruple-ζ Quality: (aug-)RPF-4Z. I. The s- and p-Block Elements.

This study reports a new relativistic prolapse-free Gaussian basis set series of quadruple-ζ quality, RPF-4Z, and an augmented version that includes extra diffuse functions, aug-RPF-4Z, for all the s- and p-block elements. The relativistic adapted Gaussian basis sets (RAGBSs), which are free of variational prolapse, were used as the starting primitive sets. Exponents of correlating/polarization functions were taken from a polynomial version of the generator coordinate Dirac-Fock (p-GCDF) method, in which the previously optimized RAGBS parameters are applied.

Quantum chemical DFT study of the interaction between molecular oxygen and FeN₄ complexes, and effect of the macrocyclic ligand.

Density functional theory (DFT) was used to examine the interaction between molecular oxygen (O₂) and macrocyclic iron complexes of the type FeN₄ during the formation of FeN₄--O₂ adducts. In order to understand how this interaction is affected by different macrocyclic ligands, O₂ was bonded to iron-tetraaza[14]annulene (FeTAA), iron-tetramethyl-tetraaza[14]annulene (FeTMTAA), iron-hexamethyl-tetraaza[14]annulene (FeHMTAA), iron dibenzotetraaza[14]annulene (FeDBTAA), and two iron-tetramethyl-dibenzotetraaza[14]annulene complexes (FeTMDBTAA1, FeTMDBTAA2). The ground state for FeN₄-O₂ adducts was the open-shell singlet.

Molecular features for antitrypanosomal activity of thiosemicarbazones revealed by OPS-PLS QSAR studies.

A quantitative structure-activity relationship analysis was employed to explore the relationship between the molecular structure of thiosemicarbazone analogues and the inhibition of the cysteine protease cruzain, a validated target for Chagas' disease treatment. A data set containing 53 thiosemicarbazone derivatives was used to produce a quantitative model for activity prediction of unknown compounds. Several electronic descriptors were obtained through DFT calculations, along with a large amount of Dragon descriptors.

Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity.

In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues.

A neural networks study of quinone compounds with trypanocidal activity.

This work investigates neural network models for predicting the trypanocidal activity of 28 quinone compounds. Artificial neural networks (ANN), such as multilayer perceptrons (MLP) and Kohonen models, were employed with the aim of modeling the nonlinear relationship between quantum and molecular descriptors and trypanocidal activity. The calculated descriptors and the principal components were used as input to train neural network models to verify the behavior of the nets.

Complexation of the anti-Trypanosoma cruzi drug benznidazole improves solubility and efficacy.

The ruthenium complex, trans-[Ru(Bz)(NH 3) 4SO 2](CF 3SO 3) 2 1, Bz = benznidazole ( N-benzyl-2-(2-nitro-1 H-imidazol-1-yl)acetamide), is more hydrosoluble and more active (IC 50try/1 h = 79 +/- 3 microM) than free benznidazole 2 (IC 50try/1 h > 1 mM). 1 also exhibits low acute toxicity in vitro (IC 50macrophages > 1 mM) and in vivo (400 micromol/kg < LD 50 < 600 micromol/kg) and the formation of hydroxylamine is more favorable in 1 than in 2 by 9.6 kcal/mol.

A quantum chemical and statistical study of flavonoid compounds (flavones) with anti-HIV activity.

The molecular orbital semi-empirical method AM1 was employed to calculate a set of molecular properties (variables) of 22 flavonoid compounds (flavones) with anti-HIV-1 activity and nine new compounds were proposed for anti-HIV-1 activity prediction. Pattern recognition techniques, principal component analysis (PCA), hierarchical cluster analysis (HCA), stepwise discriminant analysis (SDA) and K-nearest neighbor (KNN), were employed in order to reduce dimensionality and investigate which subset of variables could be more effective for classifying the flavones according to their degree of anti-HIV-1 activity. The PCA, HCA, SDA and KNN studies showed that the variables log P (partition coefficient), molecular volume (VOL) and electron affinity (EA) are responsible for the separation between anti-HIV-1 active and inactive compounds.