Ionic liquids posses efficiency as solvents, co-solvents or agents for applications involving biomolecules. Due to the increasing interest in systems containing proteins and ionic liquids, we hereby present results from molecular dynamics simulations on solutions containing the polypeptide melittin in pure water, in the neat ionic liquid 1-butyl-3-methyl-imidazolium acetate ([BMI][OAc]) and in the equimolar [BMI][OAc]/H2O mixture. When compared to the solutions containing the ionic liquid, melittin displays higher mobility and flexibility, lower stability and poorer secondary structure preservation in water. The intramolecular hydrogen bonds in melittin do not play a major role in the structural preservation, but intermolecular hydrogen bonds between melittin and the solvent are important. The micro-solvation of melittin demonstrates that anions and water molecules are in closer contact to melittin, whereas the cations maintain larger distances to the polypeptide. The presence of [BMI][OAc] reduces fluctuation in melittin's structure. Only small differences have been found in the structural arrangement of melittin in the neat ionic liquid and the ionic liquid/water mixture.

The zwitterions resulting from the covalent attachment of 3- or 4-hydroxy benzene to the 1,3-dimethylimidazolium cation represent basic compounds (pKa of 8.68 and 8.99 in aqueous solutions, respectively) that chemisorb in aqueous solutions 0.58 mol/mol of carbon dioxide at 1.3 bar (absolute) and 40 °C. Equimolar amounts of chemisorbed CO2 in these solutions are obtained at 10 bar and 40 °C. Chemisorption takes place through the formation of bicarbonate in the aqueous solution using imidazolium-containing phenolate. CO2 is liberated by simple pressure relief and heating, regenerating the base. The enthalpy of absorption was estimated to be -38 kJ/mol, which is about 30 % lower than the enthalpy of industrially employed aqueous solutions of MDEA (estimated at -53 kJ/mol using the same experimental apparatus). The physisorption of CO2 becomes relevant at higher pressures (>10 bar) in these aqueous solutions. Combined physio- and chemisorption of up to 1.3 mol/mol at 40 bar and 40 °C can be attained with these aqueous zwitterionic solutions that are thermally stable and can be recycled at least 20 times.

Plant RNases T2 are involved in several physiological and developmental processes, including inorganic phosphate starvation, senescence, wounding, defense against pathogens, and the self-incompatibility system. Solanaceae RNases form three main clades, one composed exclusively of S-RNases and two that include S-like RNases. We identified several positively selected amino acids located in highly flexible regions of these molecules, mainly close to the B1 and B2 substrate-binding sites in S-like RNases and the hypervariable regions of S-RNases. These differences between S- and S-like RNases in the flexibility of amino acids in substrate-binding regions are essential to understand the RNA-binding process. For example, in the S-like RNase NT, two positively selected amino acid residues (Tyr156 and Asn134) are located at the most flexible sites on the molecular surface. RNase NT is induced in response to tobacco mosaic virus infection; these sites may thus be regions of interaction with pathogen proteins or viral RNA. Differential selective pressures acting on plant ribonucleases have increased amino acid variability and, consequently, structural differences within and among S-like RNases and S-RNases that seem to be essential for these proteins play different functions.

Understanding catalysis with H-MOR involves integration between different space-time-scales observed at the reactor. It is known that ONIOM calculations only can well capture space-time-dependent phenomena at individual active sites. We overcome this limitation by combining ONIOM(ωB97X:PM6) calculations with Boltzmann-type distribution models to improve the adsorption model. The interaction of XY=CH 4 , CO, CO 2 , CH 3 OH, and (CH 3 ) 2 O with H-MOR was studied to test our model. The calculated average-values for the heat of adsorption ( ⟨∆H a ⟩ ) agree with the experimental values. It is not always true that Brønsted acid site that interacts more strongly with XY ( ⟨∆H a ⟩ << 0) is active site that predominates in reactor.

We present detailed ONIOM(omega B97X-D:PM6) calculations for the formation mechanism of novel composites combining protonic mordenites (H-MOR) with various ionic liquids: 1,3-dimethyl-imidazolium chloride [MMIm] Cl, 1-ethyl-3-methyl-imidazolium chloride [EMIm]Cl; 1-methyl-3-propyl-imidazolium chloride [PMIm]Cl; 1-butyl-3-methyl-imidazolium chloride [BMIm]Cl, 1-(2-hydroxyethyl)-3-methyl-imidazolium chloride [HEMIm] Cl, 1,3-dimethyl-1,3,2-diazasilolium chloride [MMSiN]Cl, and 1,3-dimethyl-1,3-diphospholium chloride [MMPP]Cl. The most feasible [M]-MOR formation mechanism ([M](+) = [MMIm](+), [EMIm](+), [PMIm](+), [BMIm](+), [HEMIm](+), [MMSiN](+) [MMPP](+)) involves an ion exchange at the T4O10 position favoring the isolation of a minimal number of [M](+) isomers (i.e., conformational traps). The interaction of these [M]-MOR composites with pollutant gases has afterward been evaluated. Among the studied sytems, [EMIm]-MOR and [HEMIm]-MOR present electronic and steric conditions for potential applications in gas separation, capture, and storage (H-2 and H2S). The H-MOR framework exhibits two structural conformers with the [HEMIm](+) cation in the confined space. Both, the MOR-T4O10-[HEMIm] and MOR-T4O10-[HEMIm](HB) conformers, interconvert by a dynamic equilibrium with a transition state MOR-T4O10-TS1 acting as a conformational switch (ON-OFF) that selectively recognizes and captures H2S through a plier-like conformation.

We performed classical Molecular Dynamics computer simulations to analyze solutions of the gases CO2, N-2, and CH4 in four 1-n-butyl-3-methylimidazolium-based ionic liquids (1-n-butyl-3-methylimidazolium acetate, 1-n-butyl-3-methylimidazolium prolinate, 1-n-butyl-3-methylimidazolium bromide, and 1-n-butyl-3-methylimidazolium tetrafluoroborate). Typical experimental conditions (10 bar gas pressure and room temperature) have been chosen to study mixtures of the ionic liquids with the gases at a single gas molar fraction of 0.25. Structural aspects are discussed to judge the absorption capacities of the ionic liquids. We observed that CO2 coordinates preferentially within the polar domain of the ionic liquids with the bromide and tetrafluoroborate anions presenting the best performances. The other gases, N2 and CH4, remain in the less polar domains of the ionic liquids. Cluster size analysis indicates phase separation for these two gases. Considering both, the absorption tendency and gas separation capacity of the ionic liquids, the anion is desired to be small and possessing multiple coordination sites. In this aspect, the tetrafluoroborate anion accomplished the best results.

The interaction and solvent influence on two different imidazolium based ion pairs have been investigated by molecular dynamics simulations and Nuclear Magnetic Resonance. The cations 1,2,3,4,5-pentamethyl imidazolium and 1,3,4,5-tetramethyl imidazolium were considered with the imidazolate anion to evaluate the influence of the acidic hydrogen at the position 2 of the imidazolium ring on the ion pair formation in different solvents. The selected solvents are chloroform, dichloromethane, acetone, dimethylsulfoxide, and water, covering a broad range of polarity and permittivity. The binding free energy of the ion pair was computed by umbrella sampling. We observed that, with the increase of the dielectric constant, the ion pairs become more transient being separated in water. The free energies of binding corroborate ion pair stabilization by the hydrogen bond at carbon 2 of the imidazolium cations. In dichloromethane, we obtained weaker bound ion pairs than in acetone due to intercalation of dichloromethane into the ion pair. Thus, the ion pair stability is not only a consequence of the solvent's dielectric constant, but also due to local structural details.

The simple photolysis of CO2 in aqueous solutions to generate CO and/or hydrocarbons and derivatives in the presence of a catalyst is considered to be a clean and efficient approach for utilizing CO2 as a C1 building block. Despite the huge efforts dedicated to this transformation using either semiconductors or homogeneous catalysts, only small improvements of the catalytic activity have been achieved so far. This article reports that simple aqueous solutions of organic salts-denominated as ionic liquids-can efficiently photo-reduce CO2 to CO without using photosensitizers or sacrificial agents. The system relies on the formation of the [CO2](.-) intermediate through homolytic C-C bond cleavage in a cation-CO2 adduct of imidazolium-based ionic liquids (ILs). The system continuously produced CO up to 2.88 mmol g(-1) of IL after 40 h of irradiation by using an aqueous solution of 1-n-butyl-3-methylimidazolium-2-carboxylate (BMIm.CO2) IL, representing an apparent quantum yield of 3.9 %. The organophotocatalytic principles of our system may help to develop more simple and efficient organic materials for the production of solar fuels from CO2 under mild conditions, which represents a real alternative to those based on semiconductors and homogeneous metal-based catalysts.

Prions are proteins that cause a group of invariably fatal neurodegenerative diseases, one of the most known being bovine spongiform encephalopathy. The three‐dimensional structure of PrPSc, the altered isoform of the prion protein, has not been fully elucidated yet, and studies on prion conversion mechanisms must rely on hypothetical β‐rich structures. Experimental and computational studies indicate that the use of low pH is capable to produce a gain of β‐structure content in the otherwise unstructured N‐terminal region. These in silico studies have used different PrP fragments from distinct organisms, and with different lengths and simulation protocols, making it difficult to identify the influence of the force fields on the formation of such structures. Here, we performed a systematic study of the influence of six well‐established force fields (GROMOS96 53a6, GROMOS96 43a1, AMBER99SB, AMBER99SB‐ILDN, CHARMM27, and OPLS‐AA/L) on the process of structural conversion of the Syrian hamster cellular prion protein simulated at acidic and neutral pH. From our analysis, we observe a strong dependence of the results with the different force fields employed. Additionally, only GROMOS96 53A6 and AMBER99SB force fields are capable to capture a high β‐sheet formation at acidic pH and adequately reproduce the neutral pH. In both cases, the β‐sheet elongation seems to be guided by the movement of the N‐terminal tail toward the N‐terminal of α‐helix HB under acidic condition. These results comprise the most wide‐ranging study to date correlating force fields to structural changes in the cellular prion protein. © 2018 Wiley Periodicals, Inc.

A series of functionalized N-alkylimidazolium based ionic liquids (ImILs) were designed, through anion (carboxylates and halogenated) and cation (N-alkyl side chains) structural modifications, and studied as potential sorbents for CO2 . The sorption capacities of as prepared bare ImILs could be enhanced from 0.20 to 0.60 molar fraction by variation of cation-anion-CO2 and IL-CO2 -water interaction. By combining NMR spectroscopy with molecular dynamics simulations, a good description of interactions between ImIL and CO2 can be obtained. Three types of CO2 sorption modes have been evidenced depending on the structure of the ImIL ion pair: Physisorption, formation of bicarbonate, and covalent interaction through the nucleophilic addition of CO2 to the cation or anion. The highest CO2 sorption capacity was observed with the ImIL containing the 1-n-butyl-3-methylimidazolium cation associated with the carboxylate anions (succinate and malonate). This study provides helpful clues for better understanding the structure-activity relationship of this class of materials and the ion pair influence on CO2 capture.

The acetylation of glycerol was achieved with high conversion and selectivity towards triacetin at low temperatures and short reaction times by using acidic imidazolium salts as catalysts. Moreover, the addition of a nitro group to the imidazolium cation affords a much more competent catalyst, indicating a significant effect provided by the simple electronic change in the imidazolium cation. Theoretical calculations revealed increased polarization of the acidic hydrogen bond on the nitrated salts, which may be related to their superior catalytic behavior when compared to the non-functionalized salts. Combining the preliminary experimental and theoretical results, it is possible to suppose that the catalytic activity of acidic imidazolium salts may be better comprehended by its Bronsted acidities, but other parameters such as hardness, electronegativity, electrophilicity and ion-pair binding energy were also evaluated in order to investigate their effects in the acetylation of glycerol promoted by these acidic imidazolium salts.

The rational synthesis of alternative materials is highly demanding due to the outbreak of infectious diseases and resistance to antibiotics. Herein, we report a tailored nanoantibiotic synthesis protocol where the antibiotic binding was optimized on the silver-silica core-shell nanoparticles surface to maximize biological responses. The obtained silver nanoparticles coated with mesoporous silica functionalized with ampicillin presented remarkable antimicrobial effects against susceptible and antibiotic-resistant Escherichia coli. In addition, these structures were not cell-death inducers and different steps of the mitotic cell cycle (prophase, anaphase and metaphase) were clearly identified. The superior biological results were attributed to a proper and tailored synthesis strategy.

Emodin is one of the most abundant anthraquinone derivatives found in nature. It is the active principle of some traditional herbal medicines with known biological activities. In this work, we combined experimental and theoretical studies to reveal information about location, orientation, interaction and perturbing effects of Emodin on lipid bilayers, where we have taken into account the neutral form of the Emodin (EMH) and its anionic/deprotonated form (EM−). Using both UV/Visible spectrophotometric techniques and molecular dynamics (MD) simulations, we showed that both EMH and EM− are located in a lipid membrane. Additionally, using MD simulations, we revealed that both forms of Emodin are very close to glycerol groups of the lipid molecules, with the EMH inserted more deeply into the bilayer and more disoriented relative to the normal of the membrane when compared with the EM−, which is more exposed to interfacial water. Analysis of several structural properties of acyl chains of the lipids in a hydrated pure DMPC bilayer and in the presence of Emodin revealed that both EMH and EM− affect the lipid bilayer, resulting in a remarkable disorder of the bilayer in the vicinity of the Emodin. However, the disorder caused by EMH is weaker than that caused by EM−. Our results suggest that these disorders caused by Emodin might lead to distinct effects on lipid bilayers including its disruption which are reported in the literature.

Molecular dynamic simulations were carried out to analyze the structure of contact ion pairs containing the imidazolate anion and a variety of methyl substituted 1,3-dimethyl-imidazolium cations in chloroform solution. These ionic liquids were studied under the condition of infinite dilution. The study focused on determining the importance and the effect of different methylations at the cation's imidazolium ring. The structural analysis by radial and spatial distribution functions demonstrated that a stable contact pair is formed in chloroform along the entire simulation period. The cations are localized preferentially above or below the anion's plane ring, reflecting contributions of π+-π− stacking interaction between the two aromatic planar ions. The most acidic hydrogen at position C2 of the imidazolium cation exhibits the strongest structural correlations, at distances within the range of hydrogen bonding, with the imidazolate anion. Methylations at all the cation's ring positions in general weakened the structural correlations. For the methylation at the cation's C2, the difference in the free energy of association has been determined from potential of mean-force calculations in the order of 13kJ/mol favoring the ion pair containing the protonated C2 atom.

Bulk ionic liquids (ILs) have been widely studied by experimental and computational methodologies, due to their enormous variety of potential applications [1, 2, 3]. The imidazolium (Im) group and its derivates have been of large interest, among the large spectrum of organic cations that might compose/form ILs, also for the possibility of tailoring the ILs thermodynamic and physical properties by alkyl substitutions at different locations [2, 4]. The supermolecular structure of neat ImILs, and consequently their properties, are directly linked to the three-dimensional arrangement of cations and anions. The interplay of the three intermolecular forces, electrostatics, dispersive, and hydrogen bonding, controls the organization of the ImIL in the gas and the liquid phases [4, 5, 6, 7]. More recently, it became of interest to understand cation-anion contact ion pairs when the IL is dissolved in other solvents [8, 9] and to characterize the structure and intermolecular interactions in these intimate ion pairs. The structure of contact ion pairs containing the imidazolate anion and a variety of six methyl substituted 1,3dimethyl-imidazolium cations in chloroform solution were studied by molecular dynamic simulations in the present work. These ionic liquids were studied under the condition of infinite dilution, that means, only one ion pair. This study focused on determining the importance and the effect of different methylations at the cation’s imidazolium ring. The novelty of the work also consists in the fact of having an organic molecule, the imidazolate, as counter-ion, instead of the common chloride or hexafluoroborate. The formation of a stable contact pair in chloroform along the entire simulation period was demonstrated by radial and spatial distribution functions (Figure 1). The cations are localized preferentially above or below the anion’s plane ring, reflecting contributions of π+-π− stacking interaction between the two aromatic planar ions. The most acidic hydrogen at position C2 of the imidazolium cation exhibits the strongest structural correlations with the imidazolate anion, at distances within the range of hydrogen bonding. The structural correlations was in general weakened by methylations at all the cation’s ring positions., The difference in the free energy of association for the methylation at the cation’s C2 has been determined in the order of 13 kJ/mol from potential of mean-force calculations, favoring the ion pair containing the protonated C2 atom. 12 a 17/Nov, 2017, Águas de Lindóia/SP, Brasil Figure 1. SDFs of the six different functionalized cations studied around the imidazolate anion (at the center, view from the C4 and C5 side). Upper row: cations with hydrogen at C2 of the imidazolium ring; lower row: the corresponding cations with a methyl group at C2. The SDFs depict the same isodensity surface for all the pairs. Key-words: Imidazolium Ionic Liquid, Contact Pair, Methyl group substitution Click here to enter text. Support: This work has been supported by CNPq and CAPES References: [1] P. Wasserscheid, Nature, 439, 797 (2006). [2] A.A. Pádua, M.F. Costa Gomes, J.N. Canongia Lopes, Acc. Chem. Res. 40, 1087– 1096 (2007). [3] M. Smiglak, J.M. Pringle, X. Lu, L. Han, S. Zhang, H. Gao, D.R. Mac-Farlane, R.D. Rogers, Chem. Commun. 50, 9228–9250 (2014). [4] R.M. Lynden-Bell, M.G. Del Po ́polo, T.G. Youngs, J. Kohanoff, C.G. Hanke, J.B. Harper, C.C. Pinilla, Acc. Chem. Res. 40, 1138–1145 (2007). 
 [5] J. Dupont, J. Braz. Chem. Soc., 15, 341–350 (2004). [6] M.N. Garaga, M. Nayeri, A. Martinelli, , J. Mol. Liq., 210, 169–177 (2015). [7] R. Hayes, G.G. Warr, R. Atkin, Chem. Rev., 115, 6357–6426 (2015). 
 [8] K. Fumino, P. Stange, V. Fossog, R. Hempelmann, R. Ludwig, Angew. Chem. Int. Ed., 52, 12439–12442 (2013). [9] M. Zanatta, A.L. Girard, N.M. Simon, G. Ebeling, H.K. Stassen, P.R. Livotto, F.P. dos Santos, J. Dupont, Angew. Chem. Int. Ed., 53, 12817–12821 (2014).

It is well known that the macroscopic physico-chemical properties of ionic liquids (ILs) are influenced by the presence of water that strongly interferes with the supramolecular organization of these fluids. However, little is known about the function of water traces within this confined space and restricted ionic environments, i.e. between cations and anions. Using specially designed ILs namely 1,2,3-trimethyl-1H-imidazol-3-ium imidazol-1-ide (MMMI·Im) and 3-n-butyl-1,2-dimethyl-1H-imidazol-3-ium imidazol-1-ide (BMMI·Im), the structure and function of water have been determined in condensed, solution and gas phases by X-ray diffraction studies, NMR, molecular dynamics simulations (MDS) and DFT calculations. In the solid state the water molecule is trapped inside the ionic network (constituted of contact ion pairs formed by π(+)-π(-) interaction) through strong H-bonds involving the water hydrogens and the nitrogens of two imidazolate anions forming a guest@host supramolecular structure. A similar structural arrangement was corroborated by DFT calculations and MDS. The presence of a guest@host species (H2O@ILpair) is maintained to a great extent even in solution as detected by (1)H-(1)H NOESY-experiments of the ILs dissolved in solvents with low and high dielectric constants. This confined water catalyses the H/D exchange with other substrates containing acidic-H such as chloroform.

The formation, stabilisation and reactivity of contact ion pairs of non-protic imidazolium ionic liquids (ILs) in solution are conceptualized in light of selected experimental evidence as well theoretical calculations reported mainly in the last ten years. Electric conductivity, NMR, ESI-MS and IR data as well as theoretical calculations support not only the formation of contact ion pairs in solution, but also the presence of larger ionic and neutral aggregates even when dissolved in solvents with relatively high dielectric constants, such as acetonitrile and DMSO. The presence of larger imidazolium supramolecular aggregates is favoured at higher salt concentrations in solvents of low dielectric constant for ILs that contain shorter N-alkyl side chains associated with anions of low coordination ability. The stability and reactivity of neutral contact species are also dependent on the nature of the anion, imidazolium substituents, and are more abundant in ILs containing strong coordinating anions, in particular those that can form charge transfer complexes with the imidazolium cation. Finally, some ILs display reactivities as contact ion pairs rather than solvent-separated ions.

1-n-Butyl-2,3-dimethylimidazolium (BMMI) ionic liquids (ILs) associated with different anions undergo H/D exchange preferentially at 2-Me group of the imidazolium in deuterated solvents. This process is mainly related to the existence of ion pairs rather than the anion basicity. The H/D exchange occurs in solvents (CDCl3 and MeCN for instance) in which intimate contact ion pairs are present and the anion possesses a labile Hin its structure, such as hydrogen carbonate and prolinate. In D2O, separated ion pairs are formed and the H/D exchange does not occur. A plausible catalytic cycle is that the IL behaves as a neutral base in the course of all H/D exchange processes. NMR experiments, density functional calculations, and molecular dynamics simulations corroborate these hypotheses.

Molecular dynamics computer simulations have been performed to identify preferred positions of the fluorescent probe PRODAN in a fully hydrated DLPC bilayer in the fluid phase. In addition to the intramolecular charge-transfer first vertical excited state, we considered different charge distributions for the electronic ground state of the PRODAN molecule by distinct atomic charge models corresponding to the probe molecule in vacuum as well as polarized in a weak and a strong dielectric solvent (cyclohexane and water). Independent on the charge distribution model of PRODAN, we observed a preferential orientation of this molecule in the bilayer with the dimethylamino group pointing toward the membrane's center and the carbonyl oxygen toward the membrane's interface. However, changing the charge distribution model of PRODAN, independent of its initial position in the equilibrated DLPC membrane, we observed different preferential positions. For the ground state representation without polarization and the in-cyclohexane polarization, the probe maintains its position close to the membrane's center. Considering the in-water polarization model, the probe approaches more of the polar headgroup region of the bilayer, with a strong structural correlation with the choline group, exposing its oxygen atom to water molecules. PRODAN's representation of the first vertical excited state with the in-water polarization also approaches the polar region of the membrane with the oxygen atom exposed to the bilayer's hydration shell. However, this model presents a stronger structural correlation with the phosphate groups than the ground state. Therefore, we conclude that the orientation of the PRODAN molecule inside the DLPC membrane is well-defined, but its position is very sensitive to the effect of the medium polarization included here by different models for the atomic charge distribution of the probe.

We report the synthesis of a series of liquid-crystalline materials based on arylaldoxime esters and the characterization of these materials by H-1, C-13 NMR, ATR/FT-IR spectroscopy and elemental analysis. The chemical stability and liquid-crystalline as well as photophysical properties of the compounds are described being dependent on the heating/cooling cycles. The changes in chemical stability and the liquid crystals properties of arylaldoxime esters were observed during these thermal cycles by IR analysis. All samples underwent a thermal degradation yielding the corresponding nitriles and carboxylic acid as evidenced by IR and H-1 NMR spectra. Due to the decomposition process, information about the mesomorphic behaviour is lost. The UV-Vis absorption spectra in solution display three absorption bands between 230 and 340 nm. The fluorescence spectra exhibit a broad and structureless emission band located at 430 nm. Ab initio calculations were performed to obtain information on the molecular structure and properties of the title compounds.