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Sadlej-Sosnowska N.,Polish National Medicines Institute
Physical Chemistry Chemical Physics

The effect of a homogeneous static electric field on the Li-benzene complex in two configurations, one with a larger Li-C6H6 distance ("loose") and one with a shorter distance ("tight"), has been investigated. The electric field has the same orientation as the direction of the dipole moments of the complexes. When the direction of the field intensity vector was the same as that of the dipole moment vector, optimization of the complex's geometry in one configuration resulted in switching it to the other one. Reversing the direction of the field then transformed the other configuration back to the original one. This switching behavior was observed beginning with the loose configuration and with the tight configuration. The geometrical and electronic parameters of the complex after four steps of the reversible switching have been calculated for a selected field intensity of 0.005 atomic units (a.u.), that is 0.257 V Å-1. © 2015 the Owner Societies. Source

Obszanska K.,Polish National Medicines Institute

Streptococcus pyogenes (GAS) is a human pathogen that causes millions of infections worldwide. Comparison between GAS strains isolated in different laboratories all over the world is often difficult. Three usually used methods have either low resolution (emm typing), are expensive (MLST) or time- and labor-consuming (PFGE). Our laboratory recently developed new, inexpensive methods of GAS typing-VF (virulence factor profiling) and PP (phage profiling). To improve the typing scheme developed for GAS, we recently proposed a new typing method. Here we present detailed protocol for MLVF analysis. Source

Carboxylic acids based on exo-substituted tria-, penta-, heptafulvenes and ethylene (acrylic acids) were examined in order to determine if they are more sensitive to the substituent effect than benzoic acid - the system originally employed by Hammett. In order to accomplish this task, all possible structural isomers of benzoic acid, tria-, penta- and heptafulvene-based carboxylic acids, acrylic and methacrylic acids substituted by 13 substiuents (BH2, CHO, CN, COCN, NO2, CF3, Me, Cl, F, OH, OMe, NH 2 and NMe2) were optimized at the B3LYP/6-311++G(d,p) level of theory, and Gibbs free energies of carboxylic group dissociation (ΔGdis) were calculated. These energies were subsequently intercorrelated, and from the slopes of linear regressions, it was estimated which system is associated with greatest changes of ΔGdis due to substitution and thus is most sensitive to the substituent effect. It was found that all fulvene-based carboxylic acids have greater range of ΔGdis change than benzoic acid, but the largest range of change was observed in the case of acrylic and methacrylic acids. The acrylic acid as the most sensitive system to substitution could replace benzoic acid for an improved version of substituent constant used to measure pi-electron substituent effect. Copyright © 2013 John Wiley & Sons, Ltd. Source

Borek A.L.,Polish National Medicines Institute

Streptococcus pyogenes (GAS) is a human pathogen that causes multiple infections worldwide. The pathogenic properties of GAS strains are often linked to the production of virulence factors such as toxins, proteases or DNases. Detection of virulence factors produced by GAS strains can be used to either determine pathogenic potential of the strain or as a rapid screening and typing method. We recently developed a method to detect simultaneously 20 GAS virulence factors (spd3, sdc, sdaB, sdaD, speB, spyCEP, scpA, mac, sic, speL, K, M, C, I, A, H, G, J, smeZ and ssa) in four low volume multiplex PCR reactions (Borek et al., 2011) and below we present a detailed protocol describing the method. Source

Szatylowicz H.,Warsaw University of Technology | Sadlej-Sosnowska N.,Polish National Medicines Institute
Journal of Chemical Information and Modeling

The energies of individual hydrogen bonds (H-bonds) in A-T and G-C Watson-Crick base pairs were calculated according to the natural bond orbital (NBO) analysis of intermolecular interactions. The extent to which individual H-bonds are helpful in holding the two base pairs together was previously investigated quantitatively by a few different approaches, and the results of the present and previous estimations were compared. The method was validated by the determination of the H-bond strength changes in A-T and G-C pairs upon the substitution of the monomer (base) by two cationic substituents; the systems for which the changes were previously anticipated based on the modifications of the H-bonds' distances. © 2010 American Chemical Society. Source

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