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Canongia Lopes J.N.,University of Lisbon | Canongia Lopes J.N.,Institute Tecnologia Quimica e Biologica | Padua A.A.H.,University Blaise Pascal | Padua A.A.H.,French National Center for Scientific Research
Theoretical Chemistry Accounts | Year: 2012

In this account, we review the process that led to the development of one of the most widely used force fields in the area of ionic liquids modeling, analyze its subsequent expansions and alternative models, and consider future routes of improvement to overcome present limitations. This includes the description and discussion of (1) the rationale behind the generic and systematic character of the Canongia Lopes & Padua (CL&P) force field, namely its built-in specifications of internal consistency, transferability, and compatibility; (2) the families of ionic liquids that have been (and continue to be) parameterized over the years and those that are the most challenging both in theoretical and applied terms; (3) the steps that lead to a correct parameterization of each type of ion and its homologous family, with special emphasis on the correct modeling of their flexibility and charge distribution; (4) the validation processes of the CL&P and other force fields; and finally (5) the compromises that have to be attained when choosing between generic or specific force fields, coarse-grain or atomistic models, and polarizable or non-polarizable methods. The application of the CL&P and other force fields to the study of ionic liquids using quantum- and statistical-mechanics methods has led to the discovery and analysis of the unique nature of their liquid phases, that is, the notion that ionic liquids are nano-segregated fluids with structural and dynamic heterogeneities at the nanoscopic scale. This successful contribution of theoretical chemistry to the field of ionic liquids will also serve as a guide throughout the ensuing discussion. © 2012 Springer-Verlag.

Groves P.,University of Ulster | Webba Da Silva M.,Institute Tecnologia Quimica e Biologica
Chemistry - A European Journal | Year: 2010

[Figure Presented] Spectroscopy on a G-string! Currently there is strong interest in the determination of the topology of nucleic acid G-quadruplexes due to their biotechnological potential and biological significance. This requires the evaluation of the strand oligomerization level. Here we demonstrate a method for routine assessment of the stoichiometry of nucleic acid quadruplexes in aqueous solutions. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bernardes C.E.S.,University of Lisbon | Minas Da Piedade M.E.,University of Lisbon | Canongia Lopes J.N.,University of Lisbon | Canongia Lopes J.N.,Institute Tecnologia Quimica e Biologica
Journal of Physical Chemistry B | Year: 2011

Several structural features of aqueous solutions of the ionic liquid 1-ethyl-3-methylimidazolium ethylsulfate were analyzed in the entire concentration range using molecular dynamics simulation results. Different analysis tools developed in-house were applied to describe the size and connectivity of different water and ion aggregates as a function of the solution concentration. Four concentration ranges - xH2O < 0.5, 0.5 < xH2O < 0.8, 0.8 < xH2O < 0.95, and x H2O > 0.95 - with four distinct structural regimes - isolated water molecules, chain-like water aggregates, bicontinuous system, and isolated ions or small ion clusters - were identified and discussed, including two different percolation limits: that of water in the ionic liquid network (around xH2O = 0.8) and that of the ionic liquid in water (around xH2O = 0.95). © 2011 American Chemical Society.

Jimenez P.N.,Instituto Gulbenkian Of Ciencia | Jimenez P.N.,University of Groningen | Koch G.,University of Groningen | Koch G.,University of Wurzburg | And 5 more authors.
Microbiology and Molecular Biology Reviews | Year: 2012

Cell-to-cell communication is a major process that allows bacteria to sense and coordinately react to the fluctuating conditions of the surrounding environment. In several pathogens, this process triggers the production of virulence factors and/or a switch in bacterial lifestyle that is a major determining factor in the outcome and severity of the infection. Understanding how bacteria control these signaling systems is crucial to the development of novel antimicrobial agents capable of reducing virulence while allowing the immune system of the host to clear bacterial infection, an approach likely to reduce the selective pressures for development of resistance. We provide here an up-to-date overview of the molecular basis and physiological implications of cell-to-cell signaling systems in Gram-negative bacteria, focusing on the well-studied bacterium Pseudomonas aeruginosa. All of the known cell-to-cell signaling systems in this bacterium are described, from the most-studied systems, i.e., N-acyl homoserine lactones (AHLs), the 4-quinolones, the global activator of antibiotic and cyanide synthesis (GAC), the cyclic di-GMP (c-di-GMP) and cyclic AMP (cAMP) systems, and the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), to less-well-studied signaling molecules, including diketopiperazines, fatty acids (diffusible signal factor [DSF]-like factors), pyoverdine, and pyocyanin. This overview clearly illustrates that bacterial communication is far more complex than initially thought and delivers a clear distinction between signals that are quorum sensing dependent and those relying on alternative factors for their production. Copyright © 2012, American Society for Microbiology. All Rights Reserved.

Pereira J.F.B.,University of Aveiro | Rebelo L.P.N.,Institute Tecnologia Quimica e Biologica | Rogers R.D.,University of Alabama | Coutinho J.A.P.,University of Aveiro | And 2 more authors.
Physical Chemistry Chemical Physics | Year: 2013

This work reveals, for the first time, that polymer-ionic-liquid-based aqueous biphasic systems (ABS) exhibit a much wider hydrophilic-hydrophobic range than conventional systems reported to date. Three probe dyes were used to demonstrate that either the polymer-rich or the ionic-liquid-rich layer can serve as the most hydrophobic phase. It was found that the phase polarities can be easily tuned by the choice of an appropriate ionic liquid. © 2013 The Owner Societies.

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