Multiple linear regression models for predicting the n­octanol/water partition coefficients in the SAMPL7 blind challenge.

A multiple linear regression model called MLR-3 is used for predicting the experimental n-octanol/water partition coefficient (log PN) of 22 N-sulfonamides proposed by the organizers of the SAMPL7 blind challenge. The MLR-3 method was trained with 82 molecules including drug-like sulfonamides and small organic molecules, which resembled the main functional groups present in the challenge dataset. Our model, submitted as "TFE-MLR", presented a root-mean-square error of 0.58 and mean absolute error of 0.41 in log P units, accomplishing the highest accuracy, among empirical methods and also in all submissions based on the ranked ones. Overall, the results support the appropriateness of multiple linear regression approach MLR-3 for computing the n-octanol/water partition coefficient in sulfonamide-bearing compounds. In this context, the outstanding performance of empirical methodologies, where 75% of the ranked submissions achieved root-mean-square errors < 1 log P units, support the suitability of these strategies for obtaining accurate and fast predictions of physicochemical properties as partition coefficients of bioorganic compounds.

High-Throughput Docking Using Quantum Mechanical Scoring.

Today high-throughput docking is one of the most commonly used computational tools in drug lead discovery. While there has been an impressive methodological improvement in docking accuracy, docking scoring still remains an open challenge. Most docking programs are rooted in classical molecular mechanics. However, to better characterize protein-ligand interactions, the use of a more accurate quantum mechanical (QM) description would be necessary. In this work, we introduce a QM-based docking scoring function for high-throughput docking and evaluate it on 10 protein systems belonging to diverse protein families, and with different binding site characteristics. Outstanding results were obtained, with our QM scoring function displaying much higher enrichment (screening power) than a traditional docking method. It is acknowledged that developments in quantum mechanics theory, algorithms and computer hardware throughout the upcoming years will allow semi-empirical (or low-cost) quantum mechanical methods to slowly replace force-field calculations. It is thus urgently needed to develop and validate novel quantum mechanical-based scoring functions for high-throughput docking toward more accurate methods for the identification and optimization of modulators of pharmaceutically relevant targets.

Reference evapotranspiration during rainy and dry seasons in Mossoró, RN, Brazil / Evapotranspiração de referência nos períodos chuvoso e seco em Mossoró-RN

Mossoró, RN, Brazil, is considered one of the fruit growing centers of the Northeast region. This municipality has a persistent water deficit, with the need to develop irrigated agriculture with efficient water use and rational management of irrigation. The objective of this study was to evaluate estimation methods of reference evapotranspiration (ETo) for different climate conditions of Mossoró, comparing them with the standard Penman-Monteith-FAO 56 method. A daily data series of two distinct years, a rainy (2011) and a dry year (2012), was used. The data were obtained from the weather station of the Federal Rural University of the Semi-Arid Region (UFERSA). An analysis was performed to identify methods that best fit those of Penman-Monteith-FAO 56, and for this, ten methods were evaluated using statistical indices. The Penman-Original, Radiation-Temperature, and Hargreaves-Original methods stood out and satisfactorily met ETo estimation for the rainy season, while the Jensen-Haise, Radiation-Temperature, and Hargreaves-Original methods achieved satisfactory performance for the dry season. The Hargreaves-Samani method did not demonstrate viability in the use of ETo estimation, as it was the worst method in both studied periods and is not recommended for irrigation management.

O município de Mossoró-RN é considerado uns dos polos fruticultores da região Nordeste. O município apresenta constante déficit hídrico, sendo necessário o desenvolvimento da agricultura irrigada com o uso eficiente da água, sendo fundamental o manejo racional da irrigação. Este trabalho objetivou avaliar para as condições climáticas de Mossoró-RN, diferentes métodos de estimativa da evapotranspiração de referência (ETo), comparando-os com o método padrão de Penman-Monteith-FAO 56. Foi utilizada uma série de dados diários de dois anos distintos, um ano chuvoso (2011) e outro seco (2012). Os dados foram obtidos na estação meteorológica da Universidade Federal Rural do Semi-Árido (UFERSA). Foi realizada análise visando identificar os métodos que melhor se ajustam ao de Penman-Monteith-FAO 56, e para isto, foram avaliados 10 métodos mediante índices estatísticos. Destacaram-se os métodos de Penman-Original, Radiação-Temperatura e Hargreaves-Original, os quais atenderam satisfatoriamente a estimativa da ETo para o período chuvoso, enquanto que os métodos de Jensen-Haise, Radiação-Temperatura e Hargreaves-Original obtiveram desempenho satisfatório para o período seco. O método de Hargreaves-Samani não demonstrou viabilidade na utilização de estimativa da ETo, pois foi o pior método em ambos os períodos estudados, não sendo recomendado para o manejo da irrigação.

Reference evapotranspiration during rainy and dry seasons in Mossoró, RN, Brazil / Evapotranspiração de referência nos períodos chuvoso e seco em Mossoró-RN

Mossoró, RN, Brazil, is considered one of the fruit growing centers of the Northeast region. This municipality has a persistent water deficit, with the need to develop irrigated agriculture with efficient water use and rational management of irrigation. The objective of this study was to evaluate estimation methods of reference evapotranspiration (ETo) for different climate conditions of Mossoró, comparing them with the standard Penman-Monteith-FAO 56 method. A daily data series of two distinct years, a rainy (2011) and a dry year (2012), was used. The data were obtained from the weather station of the Federal Rural University of the Semi-Arid Region (UFERSA). An analysis was performed to identify methods that best fit those of Penman-Monteith-FAO 56, and for this, ten methods were evaluated using statistical indices. The Penman-Original, Radiation-Temperature, and Hargreaves-Original methods stood out and satisfactorily met ETo estimation for the rainy season, while the Jensen-Haise, Radiation-Temperature, and Hargreaves-Original methods achieved satisfactory performance for the dry season. The Hargreaves-Samani method did not demonstrate viability in the use of ETo estimation, as it was the worst method in both studied periods and is not recommended for irrigation management.(AU)

O município de Mossoró-RN é considerado uns dos polos fruticultores da região Nordeste. O município apresenta constante déficit hídrico, sendo necessário o desenvolvimento da agricultura irrigada com o uso eficiente da água, sendo fundamental o manejo racional da irrigação. Este trabalho objetivou avaliar para as condições climáticas de Mossoró-RN, diferentes métodos de estimativa da evapotranspiração de referência (ETo), comparando-os com o método padrão de Penman-Monteith-FAO 56. Foi utilizada uma série de dados diários de dois anos distintos, um ano chuvoso (2011) e outro seco (2012). Os dados foram obtidos na estação meteorológica da Universidade Federal Rural do Semi-Árido (UFERSA). Foi realizada análise visando identificar os métodos que melhor se ajustam ao de Penman-Monteith-FAO 56, e para isto, foram avaliados 10 métodos mediante índices estatísticos. Destacaram-se os métodos de Penman-Original, Radiação-Temperatura e Hargreaves-Original, os quais atenderam satisfatoriamente a estimativa da ETo para o período chuvoso, enquanto que os métodos de Jensen-Haise, Radiação-Temperatura e Hargreaves-Original obtiveram desempenho satisfatório para o período seco. O método de Hargreaves-Samani não demonstrou viabilidade na utilização de estimativa da ETo, pois foi o pior método em ambos os períodos estudados, não sendo recomendado para o manejo da irrigação.(AU)

Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization.

Today computational chemistry is a consolidated tool in drug lead discovery endeavors. Due to methodological developments and to the enormous advance in computer hardware, methods based on quantum mechanics (QM) have gained great attention in the last 10 years, and calculations on biomacromolecules are becoming increasingly explored, aiming to provide better accuracy in the description of protein-ligand interactions and the prediction of binding affinities. In principle, the QM formulation includes all contributions to the energy, accounting for terms usually missing in molecular mechanics force-fields, such as electronic polarization effects, metal coordination, and covalent binding; moreover, QM methods are systematically improvable, and provide a greater degree of transferability. In this mini-review we present recent applications of explicit QM-based methods in small-molecule docking and scoring, and in the calculation of binding free-energy in protein-ligand systems. Although the routine use of QM-based approaches in an industrial drug lead discovery setting remains a formidable challenging task, it is likely they will increasingly become active players within the drug discovery pipeline.

Thermodynamic analysis of fuels in gas phase: ethanol, gasoline and ethanol - gasoline predicted by DFT method.

This paper presents a theoretical study using density functional theory to calculate thermodynamics properties of major molecules compounds at gas phase of fuels like gasoline, ethanol, and gasoline-ethanol mixture in thermal equilibrium on temperature range up to 1500 K. We simulated a composition of gasoline mixture with ethanol for a thorough study of thermal energy, enthalpy, Gibbs free energy, entropy, heat capacity at constant pressure with respect to temperature in order to study the influence caused by ethanol as an additive to gasoline. We used semi-empirical computational methods as well in order to know the efficiency of other methods to simulate fuels through this methodology. In addition, the ethanol influence through the changes in percentage fractions of chemical energy released in combustion reaction and the variations on thermal properties for autoignition temperatures of fuels was analyzed. We verified how ethanol reduces the chemical energy released by gasoline combustion and how at low temperatures the gas phase fuels in thermal equilibrium have similar thermodynamic behavior. Theoretical results were compared with experimental data, when available, and showed agreement. Graphical Abstract Thermodynamic analysis of fuels in gas phase.

Experimental and theoretical binding affinity between polyvinylpolypyrrolidone and selected phenolic compounds from food matrices.

Polyvinylpolypyrrolidone (PVPP) is a fining agent, widely used in winemaking and brewing, whose mode of action in removing phenolic compounds has not been fully characterised. The aim of this study was to evaluate the experimental and theoretical binding affinity of PVPP towards six phenolic compounds representing different types of phenolic species. The interaction between PVPP and phenolics was evaluated in model solutions, where hydroxyl groups, hydrophobic bonding and steric hindrance were characterised. The results of the study indicated that PVPP exhibits high affinity for quercetin and catechin, moderate affinity for epicatechin, gallic acid and lower affinity for 4-methylcatechol and caffeic acid. The affinity has a direct correlation with the hydroxylation degree of each compound. The results show that the affinity of PVPP towards phenols is related with frontier orbitals. This work demonstrates a direct correlation between the experimental affinity and the interaction energy calculations obtained through computational chemistry methods.

Desempenho de métodos de estimativa da evapotranspiração de referência nas localidades de Frederico Westphalen e Palmeira das Missões, RS / Perfomance of methods for estimating reference evapotranspiration in the municipalities of Frederico Westphalen and Palmeira das Missões, State of Rio Grande do Sul, Brazil

A estimativa da evapotranspiração de referência (ETo), usada no balanço hídrico, possibilita quantificar o armazenamento de água no solo, auxiliando no manejo da irrigação. O objetivo do trabalho foi comparar métodos mais simples de estimativa da evapotranspiração de referência com o método Penman-Monteith (FAO), nas escalas diária e de 5, 10, 15 e 30 dias, e mensal, para os municípios de Frederico Westphalen e Palmeira das Missões, no RS. Os métodos avaliados tenderam a melhorar a eficiência com o aumento da escala temporal de estudo, mantendo o mesmo desempenho para ambas as localidades. Os maiores e menores valores de ETo ocorreram nos meses de dezembro e junho, respectivamente. A maioria dos métodos subestimou os valores de ETo. Em qualquer escala temporal, os métodos de Makking e da Radiação FAO24 podem substituir o modelo de Penman-Monteith.

The estimation of reference evapotranspiration (ETo), used in water balance, allows to determine soil water content, assisting on irrigation management. The present study aimed to compare simple ETo estimating methods with the Penman-Monteith (FAO), in the folowing time scales: daily, 5, 10, 15 and 30 days and monthly in the counties of Frederico Westphalen and Palmeira das Missões, in the Rio Grande do Sul state, Brazil. The methods tested had their efficiency improved by increasing the time scale of analysis, keeping the same performance for both locations. The highest and lowest ETo values occurred in December and June, respectively. Most methods underestimated ETo. For any of the time scales Makking and Radiaton FAO24 methods can replace the Penman-Monteith for estimating ETo.

Desempenho de métodos de estimativa da evapotranspiração de referência nas localidades de Frederico Westphalen e Palmeira das Missões, RS

The estimation of reference evapotranspiration (ETo), used in water balance, allows to determine soil water content, assisting on irrigation management. The present study aimed to compare simple ETo estimating methods with the Penman-Monteith (FAO), in the folowing time scales: daily, 5, 10, 15 and 30 days and monthly in the counties of Frederico Westphalen and Palmeira das Missões, in the Rio Grande do Sul state, Brazil. The methods tested had their efficiency improved by increasing the time scale of analysis, keeping the same performance for both locations. The highest and lowest ETo values occurred in December and June, respectively. Most methods underestimated ETo. For any of the time scales Makking and Radiaton FAO24 methods can replace the Penman-Monteith for estimating ETo.

A estimativa da evapotranspiração de referência (ETo), usada no balanço hídrico, possibilita quantificar o armazenamento de água no solo, auxiliando no manejo da irrigação. O objetivo do trabalho foi comparar métodos mais simples de estimativa da evapotranspiração de referência com o método Penman-Monteith (FAO), nas escalas diária e de 5, 10, 15 e 30 dias, e mensal, para os municípios de Frederico Westphalen e Palmeira das Missões, no RS. Os métodos avaliados tenderam a melhorar a eficiência com o aumento da escala temporal de estudo, mantendo o mesmo desempenho para ambas as localidades. Os maiores e menores valores de ETo ocorreram nos meses de dezembro e junho, respectivamente. A maioria dos métodos subestimou os valores de ETo. Em qualquer escala temporal, os métodos de Makking e da Radiação FAO24 podem substituir o modelo de Penman-Monteith.

Desempenho de métodos de estimativa da evapotranspiração de referência nas localidades de Frederico Westphalen e Palmeira das Missões, RS

The estimation of reference evapotranspiration (ETo), used in water balance, allows to determine soil water content, assisting on irrigation management. The present study aimed to compare simple ETo estimating methods with the Penman-Monteith (FAO), in the folowing time scales: daily, 5, 10, 15 and 30 days and monthly in the counties of Frederico Westphalen and Palmeira das Missões, in the Rio Grande do Sul state, Brazil. The methods tested had their efficiency improved by increasing the time scale of analysis, keeping the same performance for both locations. The highest and lowest ETo values occurred in December and June, respectively. Most methods underestimated ETo. For any of the time scales Makking and Radiaton FAO24 methods can replace the Penman-Monteith for estimating ETo.

A estimativa da evapotranspiração de referência (ETo), usada no balanço hídrico, possibilita quantificar o armazenamento de água no solo, auxiliando no manejo da irrigação. O objetivo do trabalho foi comparar métodos mais simples de estimativa da evapotranspiração de referência com o método Penman-Monteith (FAO), nas escalas diária e de 5, 10, 15 e 30 dias, e mensal, para os municípios de Frederico Westphalen e Palmeira das Missões, no RS. Os métodos avaliados tenderam a melhorar a eficiência com o aumento da escala temporal de estudo, mantendo o mesmo desempenho para ambas as localidades. Os maiores e menores valores de ETo ocorreram nos meses de dezembro e junho, respectivamente. A maioria dos métodos subestimou os valores de ETo. Em qualquer escala temporal, os métodos de Makking e da Radiação FAO24 podem substituir o modelo de Penman-Monteith.

Apontamentos sobre pesquisa qualitativa e pesquisa empírico-fenomenológica

Este estudo visa apresentar, numa perspectiva teórica, a pesquisa qualitativa e o método fenomenológico, tomando por base o modelo empírico-compreensivo de Amedeo Giorgi. Na busca por minimizar as dificuldades encontradas na aplicação do método fenomenológico, no que concerne à grande variedade de interpretações, e explicitar como se constituem os resultados dessa prática de pesquisa, foi necessário esclarecer a natureza qualitativa da realidade investigada, o modelo de relação entre investigador-investigado e o modo como se obtiveram o conhecimento do problema e os aspectos intrinsecamente relacionados. Com o intuito de abranger esse conteúdo, o artigo dividiu-se em três partes. Foi feita, inicialmente, uma introdução sobre a pesquisa qualitativa; posteriormente, propôs-se discutir a fenomenologia e seus principais conceitos, e, na terceira parte deste artigo, foi estudado o método fenomenológico, em especial o modelo desenvolvido por Giorgi.(AU)

This study addressed, from a theoretical perspective, qualitative research and the phenomenological method based on the empirical-comprehensive model of Amedeo Giorgi. In an effort to minimize the difficulties found when applying the phenomenological method, in terms of the great variety of interpretations and also in explaining the manner in which the results of this kind of research are constituted, it was necessary to clarify the qualitative nature of the situation under investigation, the investigator/investigatee relationship model and the way in which an awareness of the problem has been created, as well as the related, intrinsic aspects. With the aim of embracing all this content, this paper was divided into three parts. Firstly, an introduction into qualitative research was carried out. The second part proposed a discussion on Phenomenology and its main concepts and, in the third part of this paper, with regard to qualitative research, the phenomenological method was studied, in particular the model developed by Giorgi.(AU)

Apontamentos sobre pesquisa qualitativa e pesquisa empírico-fenomenológica / Notes on qualitative research and empirical phenomenological research

Este estudo visa apresentar, numa perspectiva teórica, a pesquisa qualitativa e o método fenomenológico, tomando por base o modelo empírico-compreensivo de Amedeo Giorgi. Na busca por minimizar as dificuldades encontradas na aplicação do método fenomenológico, no que concerne à grande variedade de interpretações, e explicitar como se constituem os resultados dessa prática de pesquisa, foi necessário esclarecer a natureza qualitativa da realidade investigada, o modelo de relação entre investigador-investigado e o modo como se obtiveram o conhecimento do problema e os aspectos intrinsecamente relacionados. Com o intuito de abranger esse conteúdo, o artigo dividiu-se em três partes. Foi feita, inicialmente, uma introdução sobre a pesquisa qualitativa; posteriormente, propôs-se discutir a fenomenologia e seus principais conceitos, e, na terceira parte deste artigo, foi estudado o método fenomenológico, em especial o modelo desenvolvido por Giorgi.

This study addressed, from a theoretical perspective, qualitative research and the phenomenological method based on the empirical-comprehensive model of Amedeo Giorgi. In an effort to minimize the difficulties found when applying the phenomenological method, in terms of the great variety of interpretations and also in explaining the manner in which the results of this kind of research are constituted, it was necessary to clarify the qualitative nature of the situation under investigation, the investigator/investigatee relationship model and the way in which an awareness of the problem has been created, as well as the related, intrinsic aspects. With the aim of embracing all this content, this paper was divided into three parts. Firstly, an introduction into qualitative research was carried out. The second part proposed a discussion on Phenomenology and its main concepts and, in the third part of this paper, with regard to qualitative research, the phenomenological method was studied, in particular the model developed by Giorgi.