Entendendo Reações SN2 : teste de metodologias e exploração de fronteiras

Dissertação (mestrado)—Universidade de Brasília, Instituto de Química, Programa de Pós-Graduação em Química, 2012.O avanço das metodologias teóricas para a apreciação de fenômenos químicos tem sido bastante acentuado nas últimas décadas. Com o surgimento de métodos cada vez mais refinados, os quais possibilitam em muitos casos resultados mais precisos que os experimentais, surge a impressão equivocada que o entendimento qualitativo de determinados fenômenos deve ser posto de lado visando a obtenção numérica das quantidades em questão. Não obstante, o conhecimento qualitativo de certos fenômenos tem se provado essencial para a predição de seus caminhos completos. Dentro da química o exemplo maior pode ser dado pelos cálculos de estado de transição, nos quais as suposições corretas sobre as interações entre reagentes e produtos são essenciais para o desenvolvimento dos cálculos. Entre os métodos qualitativos, destaca-se a Teoria dos Orbitais Moleculares de Fronteira, desenvolvida por Kenichi Fukui na primeira metade do século XX, que permitiu a racionalização de um grande número de reações químicas. Nesse âmbito, Lionel Salem e Gilles Klopman, independentemente, propuseram uma equação que permitia a identificação imediata das interações presentes entre os substratos de uma reação assim como a caracterização da dominância de uma sobre a outra, sendo um trabalho pioneiro nesse sentido. O objetivo deste trabalho é testar um conjunto de técnicas para predição qualitativa de caminhos de reação, o modelo de Salem-Klopman, a análise por Orbitais de Ligação Naturais (Natural Bond Orbitals, NBO), e as grandezas da Teoria do Funcional da Densidade Conceitual, verificando a coerência de suas predições de sítios de interação entre moléculas reagentes, principalmente no que tange à reações SN2 com nucleófilos ambidentados. Quanto ao estudo de cargas atômicas serão utilizadas três metodologias diferentes de cálculo de cargas atômicas, os métodos de Mulliken, Löwdin - baseados em análise de população eletrônica - e CHELPG (CHarges from Electrostatic Potentials using a Grid based methodology), baseado em análise do potencial eletrostático. Pretende-se, também, com as informações vindas destas metodologias, testar o princípio HSAB de Pearson, que tem sido rediscutido nesses últimos anos. ______________________________________________________________________________ ABSTRACTThe description of chemical phenomena suffered a great enhancement on the last decades. Currently, theoretical methods can hold very accurate results, sometimes even better than experimental ones. This fact creates a paradigm: Is it really necessary to qualitatively predict chemical phenomena since it is possible to perform calculations with such high accuracy? Even though many chemists are tempted to answer negatively this question, it is surely positive. Transition state calculations, for example, depend heavily on qualitatively correct pictures of the interaction between reactants. Among the qualitative methods, it is imprescindible to highlight the Frontier Molecular Orbitals (FMO) theory, developed by Kenichi Fukui in the first thhalf of the 20 century and allowed the description of many chemical reactions. In this context, Lionel Salem and Gilles Klopman, independently, proposed a pioneer approach which used a now-called Salem-Klopman equation. With this formula they could identify interactions present in the system and determine which one dominates over the other, marking the beginning of the qualitative approach of understanding reaction paths. The objective of this work is to test Salem-Klopman’s, Natural Bond Orbital (NBO) analysis and Conceptual DFT quantities for the prediction of interaction sites in SN2 reactions with ambident nucleophiles. Parameters were collected from modern electronic structure calculations, with special attention to three atomic charges methodologies: Mulliken’s and Löwdin’s method based on electronic population analysis and CHELPG (CHarges from Electrostatic Potentials using a Grid based methodology). It is also intended to test Pearson’s HSAB principle whose validity is been called into question recently

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules [version 2; referees: 2 approved]

Background: Solubility is a physical property of high importance to the pharmaceutical industry, the prediction of which for potential drugs has so far been a hard task. We attempted to predict the solubility of acetylsalicylic acid (ASA) by estimating the absolute chemical potentials of its most stable polymorph and of solutions with different concentrations of the drug molecule. Methods: Chemical potentials were estimated from all-atom molecular dynamics simulations.  We used the Einstein molecule method (EMM) to predict the absolute chemical potential of the solid and solvation free energy calculations to predict the excess chemical potentials of the liquid-phase systems. Results: Reliable estimations of the chemical potentials for the solid and for a single ASA molecule using the EMM required an extremely large number of intermediate states for the free energy calculations, meaning that the calculations were extremely demanding computationally. Despite the computational cost, however, the computed value did not agree well with the experimental value, potentially due to limitations with the underlying energy model. Perhaps better values could be obtained with a better energy model; however, it seems likely computational cost may remain a limiting factor for use of this particular approach to solubility estimation.    Conclusions: Solubility prediction of drug-like solids remains computationally challenging, and it appears that both the underlying energy model and the computational approach applied may need improvement before the approach is suitable for routine use

Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

<div> <div> <div> <p>Alchemical free energy calculations are an increasingly important modern simulation technique. Contemporary molecular simulation software such as AMBER, CHARMM, GROMACS and SOMD include support for the method. Implementation details vary among those codes but users expect reliability and reproducibility, i.e. for a given molec- ular model and set of forcefield parameters, comparable free energy should be obtained within statistical bounds regardless of the code used. Relative alchemical free energy (RAFE) simulation is increasingly used to support molecule discovery projects, yet the reproducibility of the methodology has been less well tested than its absolute counter- part. Here we present RAFE calculations of hydration free energies for a set of small organic molecules and demonstrate that free energies can be reproduced to within about 0.2 kcal/mol with aforementioned codes. Achieving this level of reproducibility requires considerable attention to detail and package–specific simulation protocols, and no uni- versally applicable protocol emerges. The benchmarks and protocols reported here should be useful for the community to validate new and future versions of software for free energy calculations.</p></div></div></div

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Penilaian Kinerja Keuangan Koperasi di Kabupaten Pelalawan

This paper describe development and financial performance of cooperative in District Pelalawan among 2007 - 2008. Studies on primary and secondary cooperative in 12 sub-districts. Method in this stady use performance measuring of productivity, efficiency, growth, liquidity, and solvability of cooperative. Productivity of cooperative in Pelalawan was highly but efficiency still low. Profit and income were highly, even liquidity of cooperative very high, and solvability was good

Juxtaposing BTE and ATE – on the role of the European insurance industry in funding civil litigation

One of the ways in which legal services are financed, and indeed shaped, is through private insurance arrangement. Two contrasting types of legal expenses insurance contracts (LEI) seem to dominate in Europe: before the event (BTE) and after the event (ATE) legal expenses insurance. Notwithstanding institutional differences between different legal systems, BTE and ATE insurance arrangements may be instrumental if government policy is geared towards strengthening a market-oriented system of financing access to justice for individuals and business. At the same time, emphasizing the role of a private industry as a keeper of the gates to justice raises issues of accountability and transparency, not readily reconcilable with demands of competition. Moreover, multiple actors (clients, lawyers, courts, insurers) are involved, causing behavioural dynamics which are not easily predicted or influenced. Against this background, this paper looks into BTE and ATE arrangements by analysing the particularities of BTE and ATE arrangements currently available in some European jurisdictions and by painting a picture of their respective markets and legal contexts. This allows for some reflection on the performance of BTE and ATE providers as both financiers and keepers. Two issues emerge from the analysis that are worthy of some further reflection. Firstly, there is the problematic long-term sustainability of some ATE products. Secondly, the challenges faced by policymakers that would like to nudge consumers into voluntarily taking out BTE LEI