Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in the unprotonated form, the protein structure is very stable for ionic strengths ranging from 0 to 225 mM. Therefore, our findings support the hypothesis that the histidines constitute the hot points that induce configurational changes of E protein in acid pH, and give extra motivation to the development of new ideas for antivirus compound design.

Studies on Transformations of H-Phosphonates into DNA Analogues Containing P-S or P-C Bonds

In this thesis, mechanistic and synthetic studies on transformations of H-phosphonates into DNA analogues containing P-S or P-C bonds are described. Configurational stability of dinucleoside H-phosphonates and the stereochemical course of their sulfurisation in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) were investigated. In light of these studies, the reported stereoselective sulfurisation of dinucleoside H-phosphonates and benzoylphosphonates in the presence of DBU was proved to be incorrect. Efficient protocols for the synthesis of new nucleotide analogues with non-ionic C-phosphonate internucleotide linkages were developed. The synthesis of dinucleoside 2-pyridylphosphonates was successfully performed by a DBU-promoted reaction of H-phosphonate diesters with N-methoxypyridinium salts. The thio analogues, 2-pyridyl- and 4-pyridyl phosphonothioate diesters, could be obtained by modifying the reactions developed for their oxo counterparts. Dinucleoside 3-pyridylphosphonates were prepared via a palladium(0)-catalysed cross coupling strategy that could be extended also to the synthesis of nucleotide analogues with metal-complexing properties, i.e. terpyridyl- and bipyridylphosphonate derivatives. Oligonucleotides modified with pyridylphosphonate internucleotide linkages have been prepared and preliminary studies on their hybridisation properties and resistance towards enzymatic degradation were performed. Finally, nucleotidic units for the incorporation of pyridylphosphonate groups at the 5’-terminus of oligonucleotides were designed. Condensations of such units with a suitably protected nucleoside afforded after oxidation the expected dinucleoside (3’-5’)-phosphates with pyridylphosphonate monoester functions at the 5’-ends.

Ionic liquids in a multiscale study

Trotz des hohen Interesse an Ionischen Flüssigkeiten wird das zielgerichtete Design und die Anwendung Ionischer Flüssigkeiten durch fehlendes grundlegendes Verständnis erschwert. Deshalb wurde die Balance der molekularen Wechselwirkungen in Ionischen Flüssigkeiten studiert, um die Eigenschaften dieser zu verstehen und die Kraftfeldentwicklung im Rahmen des Multiskalenansatzes zu systematisieren. Es wurden reine Imidazolium-basierte Ionische Flüssigkeiten, Mischungen mit kleinen Molekülen und eine protische Ionische Flüssigkeit mit ab-initio-Methoden, hauptsächlich Car-Parrinello-Molekulardynamik, untersucht. Weiterhin wurden Eigenschaften der Flüssigphase mit denen von Ionenpaaren verglichen.rnIm Fokus standen die molekularen elektrostatischen Eigenschaften und es wurde gezeigt, dass Coulomb-Wechselwirkungen zu einzigartigen Charakteristika führten. So waren die Ionen-Nettoladungen stets reduziert, die molekularen Dipolmomentverteilungen sehr breit, elektronische Polarisation war entscheidend. Die elektrostatischen Eigenschaften waren allgemein lokal auf molekularen Größen- und Zeitskalen und hingen stark von Phasenzustand und Zusammensetzung ab. Für andere molekulare Eigenschaften, wie der Neigung zu dispersiven Kontakten oder Wasserstoffbrücken, wurde gezeigt, dass sie einen entscheidenden Einfluss auf die Feinstruktur Ionischer Flüssigkeiten hatten. Das Gleichgewicht der Wechselwirkungen zeigte sich auch in Leistungsspektren, die sich aus den ab-initio-Molekulardynamiksimulationen ergaben. Diese boten einen neuen Weg für den Vergleich zum Experiment und für einen Einblick in die schnelle Dynamik Ionischer Flüssigkeiten.

Solvation Structure of Uracil in Ionic Liquids

The local solvation environment of uracil dissolved in the ionic liquid 1-ethyl-3-methylimidazolium acetate has been studied using neutron diffraction techniques. At solvent:solute ratios of 3:1 and 2:1 ionic liquid:uracil, little perturbation of the ion-ion correlations compared to those of the neat ionic liquid are observed. We find that solvation of the uracil is driven predominantly by the acetate anion of the solvent. While short distance correlations exist between uracil and the imidazolium cation, the geometry of these contacts suggest that they cannot be considered as hydrogen bonds, in contrast to other studies by Araújo et al. (J. M. Araújo, A. B. Pereiro, J. N. Canongia-Lopes, L. P. Rebelo, I. M. Marrucho, J. Phys. Chem. B 2013, 117, 4109-4120). Nevertheless, this combination of interactions of the solute with both the cation and anion components of the solvents helps explain the high solubility of the nucleobase in this media. In addition, favorable uracil-uracil contacts are observed, of similar magnitude to those between cation and uracil, and are also likely to aid dissolution

Computational and experimental study of the behavior of cyano-based ionic liquids in aqueous solution

The solvation of cyano- (CN-) based ionic liquids (ILs) and their capacity to establish hydrogen bonds (H-bonds) with water was studied by means of experimental and computational approaches. Experimentally, water activity data were measured for aqueous solutions of ILs based on 1-butyl-3-methylimidazolium ([BMIM](+)) cation combined with one of the following anions: thiocyanate ([SCN](-)), dicyanamide ([DCA](-)), or tricyanomethanide ([TCM](-)), and of 1-ethyl-3-methylimidazolium tetracyanoborate ([EMIM][TCB]). From the latter data, water activity coefficients were estimated showing that [BMIM][SCN] and [BMIM][DCA], unlike [BMIM][TCM] and [EMIM][TCB], are able to establish favorable interactions with water. Computationally, the conductor like screening model for real solvents (COSMO-RS) was used to estimate the water activity coefficients which compare well with the experimental ones. From the COSMO-RS results, it is suggested that the polarity of each ion composing the ILs has a strong effect on the solvation phenomena. Furthermore, classical molecular dynamics (MD) simulations were performed for obtaining an atomic level picture of the local molecular neighborhood of the different species. From the experimental and computational data it is showed that increasing the number of CN groups in the ILs' anions does not enhance their ability to establish H-bonds with water but decreases their polarities, being [BMIM][DCA] and [BMIM][SCN] the ones presenting higher propensity to interact.

Why are some cyano-based ionic liquids better glucose solvents than water?

Among different classes of ionic liquids (ILs), those with cyano-based anions have been of special interest due to their low viscosity and enhanced solvation ability for a large variety of compounds. Experimental results from this work reveal that the solubility of glucose in some of these ionic liquids may be higher than in water – a well-known solvent with enhanced capacity to dissolve mono- and disaccharides. This raises questions on the ability of cyano groups to establish strong hydrogen bonds with carbohydrates and on the optimal number of cyano groups at the IL anion that maximizes the solubility of glucose. In addition to experimental solubility data, these questions are addressed in this study using a combination of density functional theory (DFT) and molecular dynamics (MD) simulations. Through the calculation of the number of hydrogen bonds, coordination numbers, energies of interaction and radial and spatial distribution functions, it was possible to explain the experimental results and to show that the ability to favorably interact with glucose is driven by the polarity of each IL anion, with the optimal anion being dicyanamide.

Chemical Immobilization Of Crosslinked Polymeric Ionic Liquids On Nitinol Wires Produces Highly Robust Sorbent Coatings For Solid-phase Microextraction.

Super elastic nitinol (NiTi) wires were exploited as highly robust supports for three distinct crosslinked polymeric ionic liquid (PIL)-based coatings in solid-phase microextraction (SPME). The oxidation of NiTi wires in a boiling (30%w/w) H2O2 solution and subsequent derivatization in vinyltrimethoxysilane (VTMS) allowed for vinyl moieties to be appended to the surface of the support. UV-initiated on-fiber copolymerization of the vinyl-substituted NiTi support with monocationic ionic liquid (IL) monomers and dicationic IL crosslinkers produced a crosslinked PIL-based network that was covalently attached to the NiTi wire. This alteration alleviated receding of the coating from the support, which was observed for an analogous crosslinked PIL applied on unmodified NiTi wires. A series of demanding extraction conditions, including extreme pH, pre-exposure to pure organic solvents, and high temperatures, were applied to investigate the versatility and robustness of the fibers. Acceptable precision of the model analytes was obtained for all fibers under these conditions. Method validation by examining the relative recovery of a homologous group of phthalate esters (PAEs) was performed in drip-brewed coffee (maintained at 60 °C) by direct immersion SPME. Acceptable recoveries were obtained for most PAEs in the part-per-billion level, even in this exceedingly harsh and complex matrix.

Development Of Egg Pc/cholesterol/α-tocopherol Liposomes With Ionic Gradients To Deliver Ropivacaine.

Ropivacaine (RVC) is an aminoamide local anesthetic widely used in surgical procedures. Studies with RVC encapsulated in liposomes and complexed in cyclodextrins have shown good results, but in order to use RVC for lengthy procedures and during the postoperative period, a still more prolonged anesthetic effect is required. This study therefore aimed to provide extended RVC release and increased upload using modified liposomes. Three types of vesicles were studied: (i) large multilamellar vesicle (LMV), (ii) large multivesicular vesicle (LMVV) and (iii) large unilamellar vesicle (LUV), prepared with egg phosphatidylcholine/cholesterol/α-tocopherol (4:3:0.07 mol%) at pH 7.4. Ionic gradient liposomes (inside: pH 5.5, pH 5.5 + (NH4)2SO4 and pH 7.4 + (NH4)2SO4) were prepared and showed improved RVC loading, compared to conventional liposomes (inside: pH 7.4). An high-performance liquid chromatography analytical method was validated for RVC quantification. The liposomes were characterized in terms of their size, zeta potential, polydispersion, morphology, RVC encapsulation efficiency (EE(%)) and in vitro RVC release. LMVV liposomes provided better performance than LMV or LUV. The best formulations were prepared using pH 5.5 (LMVV 5.5in) or pH 7.4 with 250 mM (NH4)2SO4 in the inner aqueous core (LMVV 7.4in + ammonium sulfate), enabling encapsulation of as much as 2% RVC, with high uptake (EE(%) ∼70%) and sustained release (∼25 h). The encapsulation of RVC in ionic gradient liposomes significantly extended the duration of release of the anesthetic, showing that this strategy could be a viable means of promoting longer-term anesthesia during surgical procedures and during the postoperative period.

Visual demonstration of the ionic strength effect in the classroom: the Debye-Hückel limiting law

The effects of ionic strength on ions in aqueous solutions are quite relevant, especially for biochemical systems, in which proteins and amino acids are involved. The teaching of this topic and more specifically, the Debye-Hückel limiting law, is central in chemistry undergraduate courses. In this work, we present a description of an experimental procedure based on the color change of aqueous solutions of bromocresol green (BCG), driven by addition of electrolyte. The contribution of charge product (z+|z-|) to the Debye-Hückel limiting law is demonstrated when the effects of NaCl and Na2SO4 on the color of BCG solutions are compared.

Evaluating resin-enamel bonds by microshear and microtensile bond strength tests: effects of composite resin

OBJECTIVES: The aims of this study were to evaluate the effect of resin composite (Filtek Z250 and Filtek Flow Z350) and adhesive system [(Solobond Plus, Futurabond NR (VOCO) and Adper Single Bond (3M ESPE)] on the microtensile (μTBS) and microshear bond strength (μSBS) tests on enamel, and to correlate the bond strength means between them. MATERIAL AND METHODS: Thirty-six extracted human molars were sectioned to obtain two tooth halves: one for μTBS and the other one for μSBS. Adhesive systems and resin composites were applied to the enamel ground surfaces and light-cured. After storage (37(0)C/24 h) specimens were stressed (0.5 mm/min). Fracture modes were analyzed under scanning electron microscopy. The data were analyzed using two-way ANOVA and Tukey's test (α=0.05). RESULTS: The correlation between tests was estimated with Pearson's product-moment correlation statistics (α =0.05). For both tests only the main factor resin composite was statistically significant (p<0.05). The correlation test detected a positive (r=0.91) and significant (p=0.01) correlation between the tests. CONCLUSIONS: The results were more influenced by the resin type than by the adhesives. Both microbond tests seem to be positive and linearly correlated and can therefore lead to similar conclusions.

Mechanistic aspects of the isomerization of Z-vinylic tellurides double bonds in the synthesis of potassium Z-vinyltrifluoroborate salts

Through direct transmetalation reaction of Z-vinylic tellurides with nBuLi was observed the unexpected isomerization of double bonds leading to potassium E-vinyltrifluoroborates salts in low to moderate yields. Using EPR spin trapping experiments the radical species that promoted the stereoinversion of Z-vinylic organometallic species during the preparation of potassium vinyltrifluoroborate salts was identified. The experiments support the proposed mechanism, which is based on the homolytic cleavage of the TenBu bond.

Synthesis of diaryl selenides using electrophilic selenium species and nucleophilic boron reagents in ionic liquids

We described herein the use of imidazolium ionic liquids [bmim]PF(6) and [bmim]BF(4) in the selective, metal and catalyst-free synthesis of unsymmetrical diaryl selenides by electrophilic substitution in arylboron reagents with arylselenium halides (Cl and Br) at room temperature. This is a general substitution reaction and it was performed with arylboronic acids or potassium aryltrifluoroborates bearing electron-withdrawing or electron-donating groups, affording the corresponding diaryl selenides in good to excellent yields. The ionic liquid [bmim][PF(6)] was easily recovered and utilized for further substitution reactions.

Ionic and Histological Studies of Salivary Glands in Rats with Diabetes and Their Glycemic State After Laser Irradiation

Objectives: To evaluate the effect of laser irradiation (LI) on the glycemic state and the histological and ionic parameters of the parotid and submandibular glands in rats with diabetes. Methods: One hundred twenty female rats were divided into eight groups. Diabetes was induced by administration of streptozotocin and confirmed later according to results of glycemia testing. Twenty-nine days after the induction, the parotid and submandibular glands of the rats were irradiated with 5, 10, and 20 J/cm(2) using a laser diode (660nm/100mW) (without diabetes: C5, C10, and C20; with diabetes: D5, D10, and D20, respectively). On the following day, the rats were euthanized, and blood glucose determined. Histological and ionic analyses were performed. Results: Rats with diabetes without irradiation (D0) showed lipid droples accumulation in the parotid gland, but accumulation decreased after 5, 10, and 20 J/cm(2) of laser irradiation. A decrease in fasting glycemia level from 358.97 +/- 56.70 to 278.33 +/- 87.98mg/dL for D5 and from 409.50 +/- 124.41 to 231.80 +/- 120.18 mg/dL for D20 (p < 0.05) was also observed. Conclusion: LI should be explored as an auxiliary therapy for control of complications of diabetes because it can alter the carbohydrate and lipid metabolism of rats with diabetes.

Phase transitions and spatially ordered counterion association in ionic-lipid membranes: A statistical model

We propose a statistical model to account for the gel-fluid anomalous phase transitions in charged bilayer- or lamellae-forming ionic lipids. The model Hamiltonian comprises effective attractive interactions to describe neutral-lipid membranes as well as the effect of electrostatic repulsions of the discrete ionic charges on the lipid headgroups. The latter can be counterion dissociated (charged) or counterion associated (neutral), while the lipid acyl chains may be in gel (low-temperature or high-lateral-pressure) or fluid (high-temperature or low-lateral-pressure) states. The system is modeled as a lattice gas with two distinct particle types-each one associated, respectively, with the polar-headgroup and the acyl-chain states-which can be mapped onto an Ashkin-Teller model with the inclusion of cubic terms. The model displays a rich thermodynamic behavior in terms of the chemical potential of counterions (related to added salt concentration) and lateral pressure. In particular, we show the existence of semidissociated thermodynamic phases related to the onset of charge order in the system. This type of order stems from spatially ordered counterion association to the lipid headgroups, in which charged and neutral lipids alternate in a checkerboard-like order. Within the mean-field approximation, we predict that the acyl-chain order-disorder transition is discontinuous, with the first-order line ending at a critical point, as in the neutral case. Moreover, the charge order gives rise to continuous transitions, with the associated second-order lines joining the aforementioned first-order line at critical end points. We explore the thermodynamic behavior of some physical quantities, like the specific heat at constant lateral pressure and the degree of ionization, associated with the fraction of charged lipid headgroups.

Ionic liquids as recycling solvents for the synthesis of magnetic nanoparticles

This work describes an easy synthesis (one pot) of MFe(2)O(4) (M = Co, Fe, Mn, and Ni) magnetic nanoparticles MNPs by the thermal decomposition of Fe(Acac)(3)/M(Acac)(2) by using BMI center dot NTf(2) (1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide) or BMI center dot PF(6) (1-n-butyl-3-methylimidazolium hexafluorophosphate) ionic liquids (ILs) as recycling solvents and oleylamine as the reducing and surface modifier agent. The effects of reaction temperature and reaction time on the features of the magnetic nanomaterials (size and magnetic properties) were investigated. The growth of the MNPs is easily controlled in the IL by adjusting the reaction temperature and time, as inferred from Fe(3)O(4) MNPs obtained at 150 degrees C, 200 degrees C and 250 degrees C with mean diameters of 8, 10 and 15 nm, respectively. However, the thermal decomposition of Fe(Acac)(3) performed in a conventional high boiling point solvent (diphenyl ether, bp 259 degrees C), under a similar Fe to oleylamine molar ratio used in the IL synthesis, does not follow the same growth mechanism and rendered only smaller NPs of 5 nm mean diameter. All MNPs are covered by at least one monolayer of oleylamine making them readily dispersible in non-polar solvents. Besides the influence on the nanoparticles growth, which is important for the preparation of highly crystalline MNPs, the IL was easily recycled and has been used in at least 20 successive syntheses.