SwissParam: a fast force field generation tool for small organic molecules.

The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand-protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol(-1), and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer-aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch.

Enseignement de la médecine de famille: nouvelles évolutions à Lausanne [Teaching family medicine in Lausanne].

The Faculty of Biology and Medicine of Lausanne has integrated education of family medicine all along its new undergraduate medical curriculum. The Institute of general medicine is in charge to implement those offers among which two are presented hereafter. In the new module "Generalism" several courses cover the specificities of the discipline as for example medical decision in the practice. A mandatory one-month internship in the medical practice offers an experiential immersion into family medicine for all students. In a meeting at the end of their internship, students discuss in group with their peers their individual experiences and are asked to identify, based on their personal experience, the general concepts of the specialty of family medicine and general practice.

An evaluation of the inorganic and organic geochemistry of the San Vicente Mississippi Valley-type zinc-lead district, central Peru: Implications for ore fluid composition, mixing processes, and sulfate reduction

Mississippi Tialley-type zinc-lead deposits and ore occurrences in the San Vicente belt are hosted in dolostones of the eastern Upper Triassic to Lower Jurassic Pucara basin, central Peru. Combined inorganic and organic geochemical data from 22 sites, including the main San Vicente deposit, minor ore occurrences, and barren localities, provide better understanding of fluid pathways and composition, ore precipitation mechanisms, Eh-pH changes during mineralization, and relationships between organic matter and ore formation. Ore-stage dark replacement dolomite and white sparry dolomite are Fe and rare earth element (REE) depleted, and Mn enriched, compared to the host dolomite. In the main deposit, they display significant negative Ce and probably Eu anomalies. Mixing of an incoming hot, slightly oxidizing, acidic brine (H2CO3 being the dominant dissolved carbon species), probably poor in REE and Fe, with local intraformational, alkaline, reducing waters explains the overall carbon and oxygen isotope variation and the distributions of REE and other trace elements in the different hydrothermal carbonate generations. The incoming ore fluid flowed through major aquifers, probably basal basin detrital units, with limited interaction with the carbonate host rocks. The hydrothermal carbonates show a strong regional chemical homogeneity, indicating access of the ore fluids by interconnected channelways near the ore occurrences. Negative Ce anomalies in the main deposit, that are absent at the district scale, indicate local ore-fluid chemical differences. Oxidation of both migrated and indigenous hydrocarbons by the incoming fluid provided the local reducing conditions necessary for sulfate reduction to H2S, pyrobitumen precipitation, and reduction of Eu3+ to Eu2+. Fe-Mn covariations, combined with the REE contents of the hydrothermal carbonates, are consistent with the mineralizing system shifting from reducing/rock-dominated to oxidizing/fluid-dominated conditions following ore deposition. Sulfate and sulfide sulfur isotopes support sulfide origin from evaporite-derived sulfate by thermochemical organic reduction; further evidence includes the presence of C-13-depleted calcite cements (similar to-12 parts per thousand delta(13)C) as sulfate pseudomorphs, elemental sulfur, altered organic matter in the host dolomite, and isotopically heavier, late, solid bitumen. Significant alteration of the indigenous and extrinsic hydrocarbons, with absent bacterial membrane biomarkers (hopanes) is observed. The light delta(34)S of sulfides from small mines and occurrences compared to the main deposit reflect a local contribution of isotopically light sulfur, evidence of local differences in the ore-fluid chemistry.

Perfil sócio-econômico dos alunos, repetência e evasão no curso de Química da UFMG

This paper describes a study about the causes for the dropout of chemistry undergraduate students at UFMG in the nineties. The students' social and economic profile was outlined. It was observed a correlation between family income and academic performance and between failure at the beginning of the course and the dropout, but it seems that family income doesn't affect markedly the dropout. The endogenous and exogenous causes contribute equally for the dropout. The authors suggest that the dropout could be significantly reduced if the endogenous causes such as large classes, inadequate curricula and programmes, poor teaching and the unapproachability on the part of the teachers were faced.

Currículo de licenciatura em química da universidade de brasília: uma proposta em implantação

This article presents the conception, principles and academic structure of the evening course leading to the formation of a Licentiate in Chemistry, at the University of Brasília. The curriculum has been carried out since the beginning of 1993. This curriculum has as its basic axis the graduation of future teachers integrated with the conceptual formation in Chemistry. Interdisciplinary actions are planned between the Chemistry Department, the Psychology Institute and the Faculty of Education so as to provide mechanisms which would allow the licenciate to acquire teaching experience along the course.

Aplicação de pigmentos de flores no ensino de química

In the present work, the pH dependent colour change of the crude flower extracts is suggested as subject in teaching chemical or acid-base equilibria, visual indicators and some aspects of spectrophotometric concepts and applications. The vegetal species used are commonly found in Brazil, and the extraction methodology proposed is inexpensive and easy to perform in secondary schools and in general chemistry or instrumental undergraduate courses. A bibliographic review about the use of vegetal extracts in chemical education and a discussion of the flower colour are also presented.

One pot obtention of a tetrabutylammonium hydroxide solution for ironporphyrin-OH- interaction studies in organic solvents

In this work we report the obtention of a tetrabutylammonium hydroxide (TBAOH) solution in acetonitrile in a one pot process in order to study the interaction ironporphyrinOH- in non-aqueous systems. All the reactions were carried out under dry argon atmosphere to prevent the contamination of the solution with CO2, which leads to the formation of (TBA)2CO3.

Uma proposta de síntese para o ensino integrado das disciplinas experimentais de química orgânica e inorgânica nos cursos de graduação

The synthesis of the layered compound VO(PO4)(H2O)2 and its use to oxidize 2-butanol to the ketone 2-butanone, is proposed as an experiment to integrate the organic and inorganic experimental undergraduate chemistry courses, in an atempt to overcome the observed disrupture between organic and inorganic chemistry.

Quatro décadas de química na UNESP/Araraquara

This article describes the history of four decades of activities in the Institute of Chemistry of Araraquara, UNESP: the beginning, the evolution of undergraduate and graduate courses and the infra-structure of teaching and research.

Relato de uma experiência pedagógica no ensino de química: formação profissional com responsabilidade ambiental

The toxic heavy metals can not be transformed in other less toxic substances as organic wastes through chemical process. Various chemistry courses at Faculty of Philosophy, Sciences and Humanities (FFCLRP/USP) use heavy metals in their experimental classes. In this context, a course were created: "Heavy Metal Wastes generated in the teaching and research laboratories: disposal or recovery" and has a specific goal to capacitate the students to define the adequate strategy for disposal or recovery of the chemical wastes, in particular heavy metals, through an interdisciplinary approaching. This course was given to 25 students during the second semester of 2000 and 2001. The environmental responsibility desired for the professional and citizen can be promoted.

A formação do Químico

Training of highly qualified personnel is the most transversal axis among those identified in the document "Mobilizing Axes in Chemistry", published by SBQ, in 2002, which demands to deep the discussions, initiated in the symposium "The Chemist's Education", whose main objective was to discuss the repercussions of that training in the teaching and in the industrial section. After the publication of an initial paper, a couple of meetings and workshops held in Rio de Janeiro, in December 2003, involving the national chemist community, discussed the "The role of the graduate degrees in the Chemist's Education" and "The Chemist's Education", and confirmed the need to invest in the formation of qualified human resources in profusion and in all levels. Actions to be taken were delineated. Presently, the graduate programs in Chemistry are showing expressive results. However, although these professionals are mostly absorbed by the academy (the absorption of the industry is less significant), only a few programs give special attention to the didactical and pedagogical training. The regional decentralization is actually a tendency in most programs, but the interaction academy-economic activities is still a challenge. It is necessary to establish with the industrial section, the highly qualified professional's profile in Chemistry that the industry can absorb. The undergraduation is growing in number and quality, however still excessively concentrated in the Southeast area. The national "Curricula Guidelines" for Chemistry Courses, through its flexible approach, propitiate the integral, interdisciplinary (non compartmentalized) and critical-reflexive training of the professionals as citizens and as entrepreneurs. However, deficiencies are still recognized. The evaluation system of undergraduate courses has been able to identify the most fragile modalities of courses and other indicators. It was also verified that Brazilian chemistry industry absorbs minimally the highly qualified professionals, which is attributed to the fact that the Federal Council of Chemistry is vertically organized and does not recognize the graduate degrees as professional qualification. In the conclusion, it stands out, among other aspects, the importance of the effective implantation of the national curricula guidelines, bringing out courses whose didactical and pedagogical projects may offer a solid formation in Chemistry, but comprehensive and general enough to enable the Chemistry professionals to develop varied skills.

A graduação em química: um novo químico para uma nova era

The discussions sponsored by the Brazilian Chemical Society, over the past five years, intending to produce a chemistry agenda with perspectives and needs for the next decade for the country, have involved the national chemistry community and several related sectors of Brazilian society. Chemistry education has been the theme throughout these discussions. It is known that the low level of basic and secondary education and the recent increase in high school courses and institutions adversely affect the quality of undergraduate teaching. The recent national "Curriculum Guidelines" for Chemistry Courses, through their flexible approach, encourage the integral, interdisciplinary (non compartmentalized) and critical-reflexive training of professionals as citizens and as entrepreneurs. However, deficiencies are still recognized. The system of undergraduate course evaluation has identified the most fragile modalities of the courses and other indicators. Also, it has been verified that the Brazilian chemistry industry absorbs only minimally the highly qualified professionals, which is attributed to the fact that the Federal Council of Chemistry is vertically organized and does not recognize the graduate degrees as professional qualifications. In conclusion, the importance of the effective implantation of the national curriculum guidelines is apparent, among other aspects, highlighting courses whose didactical and pedagogical projects may offer a solid formation in Chemistry. However, at the same time the guidelines are comprehensive and general enough to enable the chemistry professionals to develop varied skills.

A importância da Química Analítica Qualitativa nos cursos de Química das instituições de ensino superior brasileiras

The results of a survey of institutions offering undergraduate studies, with the objective of evaluating the importance of Qualitative Analytical Chemistry for Chemistry courses in Brazil, are presented and discussed. Judging by the data, the content of the course of Qualitative Analytical Chemistry is considered by the Brazilian institutions offering undergraduate studies to be a body of knowledge essential for the formation of the chemist. This aspect is deemed valid for both baccalaureate and teaching license studies.

O pKa de indicadores ácido-base e os efeitos coloidais

An experiment is proposed that can be included in undergraduate courses of chemistry. The subject is the acidity of organic compounds, which are employed as pH indicators, particularly in acid-base titrations. The indicators used are methyl orange, bromophenol blue and bromocresol green in aqueous medium. The influence of colloidal systems on the equilibrium is evaluated by the pKa. The colloids employed are surfactants like sodium dodecyl sulfate, cetyl-trimethylammonium bromide and a polymeric non-ionic F127 (pluronics). The effect of stabilization promoted by the system on the acidic or basic structureof the indicator establishes the action mechanism of the colloid on the pKa values.

Um espalhador de baixo custo de fase estacionária em placas para cromatografia em camada delgada

Chromatography is a means of separating mixtures into their several components. TLC, mainly a liquid/solid process, is one of the separation techniques most often used. It is indispensable in laboratories dealing with natural products, organic and analytical chemistry. Commercial chromatography plates are offered at relatively high cost. In this work the construction of a hand-operated plate coater of stationary phases of low cost and good reproducibility is described to be used in teaching laboratories and research.