J.C Pinheiro

A structure–activity relationship study of HEPT-analog compounds with anti-HIV activity

The molecular orbital method PM3 is employed to calculate a set of molecular descriptors (variables) for 36 deoxy analogs of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) with anti-HIV-1 activity. Pattern recognition methods, principal component analysis (PCA) and stepwise discriminant analysis (SDA) were employed in order to reduce dimensionality and investigate which subset of variables should be more effective for classifying the HEPT-analog compounds according to their degree of anti-HIV-1 activity. The PCA showed that the variables log P (partition coefficient), MR (molecular refractivity),DHf (heat of formation), QN (net atomic charge on atoms 2 and 3), and x (Mulliken’s electronegativity) are responsible for the separation between compounds with higher and lower anti-HIV-1 activity. By using the SDA we have found the following descriptors as responsible for the separation between the active and less active compounds: log P (partition coefficient), x (Mulliken’s electronegativity), m (dipole moment), Q4 (net atomic charge on atom 4), and t2 (torsional angle). From the SDA we present a prediction rule for classifying new HEPT-analog compounds with anti-HIV-1 activity. q 2000 Elsevier Science B.V. All rights reserved.

Generator coordinate Hartree–Fock method applied to the choice of a contracted Gaussian basis for the second-row atoms

The generator coordinate Hartree–Fock (GCHF) method is employed as a criterion for the selection of a 18s12p Gaussian basis for the atoms Na–Ar. The role of the weight functions in the assessment of the numerical integration range of the GCHF equations is shown. The extended basis is then contracted to (10s6p) by a standard procedure and in combination with the previously contracted (7s5p) Gaussian basis for the atoms Li–Ne is enriched with polarization functions. This basis is tested for AlF, SiO, PN, BCl, and P2. The properties of interest were HF total energies, MP2 dipolar moments, bond distances, and dissociation energies.

A multiple linear regression and partial least squares study of flavonoid compounds with anti-HIV activity

Abstract The molecular orbital semi-empirical method PM3 was employed to calculate a set of molecular properties (variables or descriptors) of 21 flavonoid compounds with anti-HIV activity. The correlation between biological activity and structural properties was obtained by using the multiple linear regression and partial least squares methods. The model obtained showed not only statistical significance but also predictive ability. The significant molecular descriptors related to the compounds with anti-HIV activity were: electronegativity (χ) and the charges on atoms C3 and C7 (Q3 and Q7, respectively). These variables led to a physical explanation of electronic molecular property contributions to HIV inhibitory potency.

The generator coordinate Hartree-Fock method applied to the choice of a contracted gaussian basis for first-row atoms

Abstract The generator coordinate Hartree-Fock (GCHF) method is employed as a criterion for the selection of an 18s 12p gaussian basis for the atoms H, Li-Ne. The role of the weight functions in the assessment of the numerical integration range of the GCHF equations is shown. The extended basis is then contracted to [5s] (H) and [7s 5p] (Li-Ne) by a standard procedure and enriched with polarization functions. This basis is tested for H2, BH, B2, C2, N2, O2, F2, HF, LiF, BeO, BF, CN−, CO and NO+. The properties of interest were HF total energies, CISD bond distances and vibrational frequencies, and MP2 dissociation energies.

Gaussian basis sets to the theoretical study of the electronic structure of perovskite (LaMnO3)

The Generator Coordinate Hartree – Fock (GCHF) method is applied to generate extended (20s14p), (30s19p13d), and (31s23p18d) Gaussian basis sets for the O, Mn, and La atoms, respectively. The role of the weight functions (WFs) in the assessment of the numerical integration range of the GCHF equations is shown. These basis sets are then contracted to [5s3p] and [11s6p6d] for O and Mn atoms, respectively, and [17s11p7d] for La atom by a standard procedure. For quality evaluation of contracted basis sets in molecular calculations, we have accomplished calculations of total and orbital energies in the Hartree– Fock – Roothaan (HFR) method for 5 MnO 1þ and 1 LaO 1þ fragments. The results obtained with the contracted basis sets are compared with values obtained with the extended basis sets. The addition of one d polarization function in the contracted basis set for O atom and its utilization with the contracted basis sets for Mn and La atoms leads to the calculations of dipole moment and total atomic charges of perovskite (LaMnO3). The calculations were performed at the HFR level with the crystal [LaMnO3]2 fragment in space group C2v: The values of dipole moment, total energy, and total atomic charges showed that it is reasonable to believe that LaMnO3 presents behaviour of piezoelectric material. q 2003 Elsevier B.V. All rights reserved.

Ab initio study of high tridymite by the formalism generator coordinate Hartree-Fock

Abstract The Generator Coordinate Hartree–Fock (GCHF) Method is applied to generate extended 14s 8p and 17s 11p Gaussian basis sets for the atoms O and Si, respectively. The role of the weight functions in the assessment of the numerical integration range of the GCHF is shown. The Gaussian basis sets are contracted to [6s4p] O atom and [8s5p] Si atom by the Dunning’s segmented contraction scheme. To evaluate the quality of our contracted [6s4p] and [8s5p] bases in molecular calculations we accomplish calculations of total and orbital energies in the Hartree–Fock–Roothaan method for O 2 and SiO molecules. We compare the results obtained with the our (14s 8p) and (17s 11p) bases sets with the of 6-311G basis and with values from the literature. The addition of one d polarization function in the silicon basis and its utilization with the basis for oxygen leads to the calculation of electronic properties and IR Spectrum of high tridymite in space group D 3d .

Gaussian basis sets by generator coordinate Hartree-Fock method to ab initio calculations of electron affinities of enolates

Fed Univ Para, Ctr Ciencias Exatas & Nat, Dept Quim, Lab Quim Teor & Computac, BR-66075110 Belem, Para, Brazil

Pattern recognition study of structure–activity relationship of halophenols and halonitrophenols against fungus T. mentagrophytes

Abstract Compounds (halophenols and halonitrophenols) with antifungal activity against the fungus species T. mentagrophytes are proposed with the aid of techniques of structure–activity relationship. Molecular parameters were calculated with quantum chemical, structure–activity relationship and quantitative structure–activity relationship programs. Principal components analysis, hierarchical cluster analysis and stepwise discriminant analysis methods showed that the parameters polarizability (Pol), heat of formation (ΔHf), lowest unoccupied orbital energy (ϵLUMO), dipole moment (μ), hydration energy (HE) and surface area (A) are responsible for the separation between the active and inactive compounds.

Development of basis sets to calculations of the electronic structure of YMnO3

Fed Univ Para, Ctr Ciencias Exatas & Nat, Dept Quim, Lab Quim Teor & Computac, BR-66075110 Belem, Para, Brazil

A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7

Since the publication of one of the first studies using 2D gel electrophoresis by Patrick H. O’Farrell in 1975, several other studies have used that method to evaluate cellular responses to different physicochemical variations. In environmental microbiology, bacterial adaptation to cold environments is a “hot topic” because of its application in biotechnological processes. As in other fields, gel-based and gel-free proteomic methods have been used to determine the molecular mechanisms of adaptation to cold of several psychrotrophic and psychrophilic bacterial species. In this review, we aim to describe and discuss these main molecular mechanisms of cold adaptation, referencing proteomic studies that have made significant contributions to our current knowledge in the area. Furthermore, we use Exiguobacterium antarcticum B7 as a model organism to present the importance of integrating genomic, transcriptomic, and proteomic data. This species has been isolated in Antarctica and previously studied at all three omic levels. The integration of these data permitted more robust conclusions about the mechanisms of bacterial adaptation to cold.