Técnicas para análise de desempenho de computadores

A series of open source benchmarks for computer performance analysis of personal computers with a focus on computational chemistry calculations is presented. The results returned by these tests are discussed and used to correlate with the actual performance of a set of computers available for research on two computing intensive fields of chemistry, quantum chemical and molecular simulation calculations.

Técnicas de análise do perfil de execução e otimização de programas em química computacional

In this paper we review the basic techniques of performance analysis within the UNIX environment that are relevant in computational chemistry, with particular emphasis on the execution profile using the gprof tool. Two case studies (in ab initio and molecular dynamics calculations) are presented in order to illustrate how execution profiling can be used to effectively identify bottlenecks and to guide source code optimization. Using these profiling and optimization techniques it was possible to obtain significant speedups (of up to 30%) in both cases.

Aspectos técnicos envolvidos na construção de um "cluster beowulf"

Beowulf cluster is perhaps the cheapest way to construct a high performance computers. The strategy of reaching a high power computing isn't so difficult, but buying and configurating should be done carefully. Technical aspects of hardware components and message-passing libraries are considered, with some results given as examples.

Modelos contínuos do solvente: fundamentos

Continuum solvation models are nowadays widely used in the modeling of solvent effects and the range of applications goes from the calculation of partition coefficients to chemical reactions in solution. The present work presents a detailed explanation of the physical foundations of continuum models. We discuss the polarization of a dielectric and its representation through the volume and surface polarization charges. The Poisson equation for a dielectric was obtained and we have also derived and discuss the apparent surface charge method and its application for free energy of solvation calculations.

A teoria de pearson para a disciplina de química orgânica: um exercício prático e teórico aplicado em sala de aula

We report a didactic experience in teaching Pearson's theory (HSAB) to graduate students in organic chemistry. This approach was based on teaching students how to use computer programs to calculate frontier orbitals (HOMO-LUMO). The suggested level of calculation was a semi-empiric PM3, proving to be efficient for obtaining robust and fast numerical results that can be performed easily in the classroom. We described a practical computational exercise and asked students to compare these numerical data with qualitative analysis using valence bond theory. A comprehensive solution of this exercise is presented, aiming to support teachers in their lessons.

The chemistry of Brazilian leguminosae. LXI. (+)-Methyl Vouacapenate from Vouacapoua pallidior

Thz wood of Vouacapoua pallidior (Leguminosae-Caesalpinioideae) Contains (+)-methyl vouacapenate.

Curare - Botany, Chemistry, and Pharmacology

Some aspects of curare research carried out over the last 25 years are discussed. Accepting a pharmacological rather than purely ethnological definition means, that curares are not limited to South America but that they are also known from Central Africa and South-EastAsia. Among the criteria that have been suggested for classifying South American curares: type of container, geographical origin, botanical sourcesof the active, constituent!, and chemical composition. A combination of botanical and geographical criteria leads to much the same regional ;groupings a combination of criteria involving the type of container and the chemical composition. The active principles in curares may derive from members of thr Loganiaceae (Strychnos) and/or Menispermaceae mainly Chondrodendron and Curarea, but also Abuta,Anomospermum, Cissampelos, Sciadotenia, and Telitoxicum). Certain of the Strychnos dimeric indole alkaloids can undergo a variety of cleavages, oxidations, and isomerizations; hence., some of the compounds obtained by normal isolation procedures one almost certainly artefacts. The different genera of, Menispermaceae a wide range of bisbenzyl and other types of isoquinoline alkaloids. Many of the plant additives also contain a variety of isoquinoline bases, and this has to be taken into account in assessing the contribution these ingredients may make to the ovzJuxll activity of, curare. Loganiaceae-bated curares with toxiferinzas major alkaloid tend to be the most toxic. In the case of Menispermaceae-based products, there-is evidence that the process by which they are made may lead to a considerable increase in the toxicity of the finished poisons as compared with the original plant materials. The mechanism of action of the alkaloids it, outlined, and the role of curare alkaloids in the development of, present-day muscle-relaxant drugs used in surgery is indicated. Attention lb drawn to reported medicinal uses of some of the alkaloid-bearing plants incorporated into curares, suggesting that further evaluation of these plants may be of interest.

The ceramic artifacts in archaeological black earth (terra preta) from Lower Amazon Region, Brazil: chemistry and geochemical evolution

This paper carried out a chemical investigation of archaeological ceramic artifacts found in archaeological sites with Black Earth (ABE) in the Lower Amazon Region at Cachoeira-Porteira, State of Pará, Brazil. The ceramic artifacts, mostly of daily use, belong to Konduri culture (from 900 to 400 years BP). They are constituted of SiO2, Al2O3, Fe2O3, Na2O and P2O5; SiO2 and Al2O3 together add up to 80 % and indicate influence of acid rocks, transformed into clay minerals basically kaolinite. The relative high contents of P2O5 (2.37 % in average) come out as (Al,Fe)-phosphate, an uncommon fact in primitive red ceramics, but found in some roman and egyptian archaeological sites. The contents of the trace elements are similar or below the Earth's crust average. This chemical composition (except P2O5) detaches saprolite material derived acid igneous rocks or sedimentary ones as the main raw material of the ceramics. The contents of K, Na and Ca represent the feldspars and rock fragments possibly introduced into saprolitic groundmass, indicated by mineralogical studies. The presence of cauixi and cariapé as well as quartz sand was confirmed by optical microscope, SEM analyses and by the high silica contents of ceramic fragments. Phosphorus was possibly incorporated into groundmass during cooking of foods, and ABE soil profile formation developed on yellow Latosols. The raw materials and its tempers (cauixi, or cariapé, feldspar, crushed rocks, old ceramic artifacts and quartz fragments) are found close to the sites and therefore and certainly came from them.

The mineralogy and chemistry of the German and Portuguese tiles used to face a historic building in the Amazon region and their natural susceptibility to tropical weathering

During the 19th century, the most prominent buildings of the city of Belém were faced entirely with tiles manufactured in Portugal and Germany, which now exhibit distinct degrees of degradation. The Pinho mansion is one of the most important of these buildings and was selected for the investigation of the action of the tropical Amazonian climate on the degradation of the tiles. To achieve this objective, the tiles were mapped for organic and inorganic degradation, and samples were collected for analysis. The minerals were determined by XRD, the chemical composition by classical wet methods and SEM/EDS, and the microorganisms under the microscope. The results show that the German and Portuguese tiles are quite different in their composition. While both ceramic bodies are composed of SiO2 and Al2O3, CaO was found only in the Portuguese tile. The low Na2O and K2O contents indicate the addition of materials to reduce the fusion temperature. SiO2 and PbO are the main constituents of the glaze, with CoO and FeO being added as pigment. The ceramic body of the German tiles is constituted of quartz, mullite, and cristobalite, in contrast with the Portuguese tiles, which are made of quartz, gehlenite, diopside, calcite, and feldspars. The glazes are XRD-amorphous. The chemical and mineralogical differences between the German and Portuguese tiles indicate that they were produced from different raw materials under distinct thermal processes. The most prominent weathering-related modifications are the thin layers (German tiles), oxidation stains, dark stains, the detachment of the tile (Portuguese tiles), loss of the glaze and powdering of the ceramic body (Portuguese tiles) through the establishment of Cyanophyta and Bacillariophyta.. The distinct degradation patterns of the tiles exposed to the tropical Amazon climate are a consequence of their distinct mineralogy and chemistry.

Some progress on the chemistry of natural bioactive terpenoids form Chinese medicinal plants

(1) Pseudolaric acids - Novel diterpenes, Pseudolaric acid A, B, C and D were isolated from Pseudolarix kaempferi Gorden (pinaceae). Their structures were assigned by spectroscopic data and chemical correlations. In the contineous studies, the absolute configurations, the conformations in the solutions, the framentation mechanisms of MS and assigments of all NMR spectral signals were also reported. They showed the antifungal and cytotoxic activities. (2) Daphnane diterpenes - In the further studies on the plants of Thymelaeaceae, besides 10 known diterpenes, 16 new daphnane diterpenes were isolated from Daphne genkwa, D. tangutica, D. giraldii, Wikstroemie chamaedaphne. They showed the antifertilities activities. (3) Tripterygium diterpenes 14 new diterpenes were isolated from Triperygium wilfordii, T. regeli and T. hypoglaucum. Some of them showed the antitumor activities. The CD spectra showed that A/B ring of all compoundshave trans configuration as same as tripdiolide and triptolide determined by X-ray diffraction (4) Pregnane glycosides from Marsdenia koi - Two new pregnane glycosides marsdenikoiside A and marsdenikoiside B which can terminate the early pregnancy were isolated from Marsdeia koi. Their structures were elucidated by hydrolysis and spectroscopic methods.

Chemistry, cytotoxicity and antileishmanial activity of the essential oil from Piper auritum

Leishmaniasis is one of the most important parasitic infections, but current treatments are unsatisfactory due to their toxicity, cost and resistance. Therefore, the development of new antileishmanial compounds is imperative. Many people who live in endemic areas use plants as an alternative to treat the disease. In this paper, we characterised the essential oil from Piper auritum, evaluated its cytotoxicity and determined its antileishmanial activity. The chromatogram obtained by gas chromatography revealed 60 peaks and we found that safrole was the most abundant compound, composing 87% of the oil. The oil was active against the promastigotes of Leishmania major, Leishmania mexicana, Leishmania braziliensis and Leishmania donovani with a favourable selectivity index against peritoneal macrophages from BALB/c mice. The Piper-oil inhibited the growing of intracellular amastigotes of L. donovani with an IC50 value of 22.3 ± 1.8 μg/mL. This study demonstrates the usefulness of the essential oils as a promising alternative to treat leishmaniasis.

Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors

Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors (NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the highly active antiretroviral therapy in combination with other anti-HIV drugs. However, the rapid emergence of drug-resistant viral strains has limited the successful rate of the anti-HIV agents. Computational methods are a significant part of the drug design process and indispensable to study drug resistance. In this review, recent advances in computer-aided drug design for the rational design of new compounds against HIV-1 RT using methods such as molecular docking, molecular dynamics, free energy calculations, quantitative structure-activity relationships, pharmacophore modelling and absorption, distribution, metabolism, excretion and toxicity prediction are discussed. Successful applications of these methodologies are also highlighted.

Comparison of microscopic method and computational program for pesticide deposition evaluation of spraying

The main objective of this work was to compare two methods to estimate the deposition of pesticide applied by aerial spraying. Hundred and fifty pieces of water sensitive paper were distributed over an area of 50 m length by 75 m width for sampling droplets sprayed by an aircraft calibrated to apply a spray volume of 32 L/ha. The samples were analysed by visual microscopic method using NG 2 Porton graticule and by an image analyser computer program. The results reached by visual microscopic method were the following: volume median diameter, 398±62 mum; number median diameter, 159±22 mum; droplet density, 22.5±7.0 droplets/cm² and estimated deposited volume, 22.2±9.4 L/ha. The respective ones reached with the computer program were: 402±58 mum, 161±32 mum, 21.9±7.5 droplets/cm² and 21.9±9.2 L/ha. Graphs of the spatial distribution of droplet density and deposited spray volume on the area were produced by the computer program.