Assessing the folding propensity of aliphatic units within helical aromatic oligoamide foldamers

Great attention is devoted to hybrid foldamers composed of more than one type of monomers. The folding of such hybrids requires units that may possess very different structures to be compatible. A method to assess this compatibility consists in studying the behavior of a monomer of one type within a sequence of another type of monomer. We have prepared and investigated the structure of flexible aliphatic monomers in the context of the rigid helices of quinoline-carboxamides. NMR and X-ray crystallography show that the rigid helical backbones may impart defined conformation into otherwise flexible units and that compatible folding modes exist between very different monomers.     

Preferential site of solvation of the furan ring in acidic solvents

A study of the correlation of solvent effects on the chemical shifts of the methyl protons of sylvan, toluene and α-picoline led to the conclusion that the preferential site of solvation of the furan ring in acidic solvents is the π-electron cloud and not the n-electron orbital of the oxygen atom.     

Temperature effect on formation of sodium cholate micelles

The micellization of sodium cholate (NaC) at 293.2, 298.2, 303.2, 308.2, and 313.2 K by cholate anion concentration was studied over the pH range from 6.0 to 7.2. Using a stepwise association model of cholate anions without bound sodium counterions, the aggregation number (nmacr;) of the cholate micelles was evaluated and found to increase with the total concentration, indicating that the stepwise association model is applicable. The nmacr; values go up and down with increasing temperature; 17 at 298.2 and 12 at 313.2 K and at 60 mM of the sodium cholate. The fluorescence of pyrene was measured in sodium cholate solution to determine the critical micelle concentration (CMC), indicating a narrow concentration range for CMC. A sodium-ion-specific electrode was used to determine a relatively low degree of counterion binding to micelles, supporting the validity of the present association model of cholate anions. The aggregation numbers evaluated at a constant ionic strength of 0.15 and at lower but variable ionic strengths were similar except for higher cholate concentrations.     

Expanding the registry of aromatic amide foldamers: folding, photochemistry and assembly using diaza-anthracene units

The synthesis of various 1,8-diaza-4,5-dialkoxy-2,7-anthracene dicarboxylic acid derivatives and their incorporation into cyclic and helically folded aromatic oligoamides are reported. The ability of the diaza-anthracene monomers to undergo photoaddition or head-to-tail photodimerization was investigated in the solid state and in solution. Quantitative conversion of a monomer diester to the corresponding head-to-tail photodimer could be achieved in the solid state without protection from oxygen. The formation of an emissive excimer between two diaza-anthracene units appended at the end of a helically folded oligomer was demonstrated. Intramolecular photodimerization was not observed in this compound, possibly due to the low thermal stability of the head-to-head photoadduct. A cyclic oligoamide composed of two diaza-anthracene and two pyridine units was shown to adopt a flat conformation and to form columnar stacks in the solid state. Longer, noncyclic oligoamides composed of one or two diaza-anthracene units were shown to adopt helical conformations that exist preferentially as double helical dimers.     

Temperature effect on solubilization of n-alkylbenzenes into sodium cholate micelles

The solubilization of n-alkylbenzenes (benzene, toluene, ethylbenzene, n-propylbenzene, n-butylbenzene, n-pentylbenzene, n-hexylbenzene) into an aqueous micellar solution of sodium cholate was carried out. Solubilizate concentrations at equilibrium were determined spectrophotometrically at 293.2, 298.2, 303.2, 308.2, and 313.2 K. The first stepwise association constants (K(1)) between solubilizate monomers and vacant micelles were evaluated from the equilibrium concentrations and found to increase with increasing hydrophobicity of the solubilizate molecules. From the Gibbs energy change for solubilization at different micelle aggregation numbers and from the molecular structure of the solubilizates, the function of sodium cholate micelles as solubilizer was discussed. Enthalpy and entropy changes of solubilization were calculated from the temperature dependence of the K(1) values, and the solubilization was found to be enthalpy-driven for the solubilizates with shorter alkyl chains. The results obtained were also compared with those for conventional aliphatic micelles.     

Preferential solvation effects in the electrochemistry and charge-transfer spectra of cyanoiron(II) complexes

The energies of the charge-transfer bands and the redox potentials of substituted cyanoiron complexes are strongly influenced by preferential solvation effects in water-acetonitrile mixed solvents, exhibiting a linear dependence with respect to the acceptor number scale. The dependence increases with the number of cyanide ligands in the complexes.     

A simple model of solvation within the molecular orbital theory

A simple model of solvation within the molecular orbital method is proposed whereby the effect of solvent molecules is simulated by the inclusion of fractional point charges at the solvent atomic centers. The method is applied to three solvation problems: the hydration of Li⁺ and F^? and the solvation effect on the interaction between NH₃ and HF. The results of the first two calculations indicate that the point charge model is capable of reliably predicting solvation energies. The calculations for H₃N···HF demonstrate that the hydration has a profound effect on the potential energy surface favoring a proton transfer structure H₃NH⁺···F^?.     

Comparative effect of cyclodextrin nanocavities versus organic solvents on the fluorescence of carbamate and indole compounds

The effect of the addition of different amounts of organic solvents (S) on the fluorescence of aromatic compounds (C) and their inclusion complexes with β-cyclodextrin (βCD) and hydroxypropyl-β-cyclodextrin (HPCD) has been examined using steady-state measurements. Carbamate pesticides with different aromatic moiety, such as carbofuran (CF), promecarb (PC), carbaryl (CY) and bendiocarb (BC) were used, as well as indole derivatives with different polarity in their lateral chains, such as melatonin (M, neutral), 5-methoxytryptamine (MT, cation) and auxin (IA, anion). Their complexes in water show a fluorescence signal higher than that obtained for the free substrates in solvent:water mixtures (30%, v/v n-propanol or acetonitrile, and 50%, v/v methanol). The isofluorescent point (IF), the %IF and the F_85% are defined in order to evaluate the use of CD nanocavities as a non-polluting alternative for the analysis of the compounds analyzed.Apparent formation constants (K_AP, M⁻¹) for the complexes of C:HPCD at different solvent percentages were determined for CF and PC with methanol (MeOH), n-propanol (ProOH) and acetonitrile (ACN), and for indole compounds with ACN. A decrease in the K_AP values for the CF:HPCD (120–30) and PC:HPCD (2000–400) complexes occurs in accordance with the solvent affinities for CDs (MeOH < ACN < ProOH). Nevertheless, in the indolic series, the polar characteristics of MT, IA and M determine their behaviour in the presence of ACN. For the neutral substrate M, K_AP decreases with the increasing percentage of ACN (100–10). In contrast, for IA and MT (ionic substrates) K_AP increases (10–100).These results may be accounted for by two different mechanisms: the competition between C and S for the cavity of the receptor or the formation of ternary complexes C:S:CD with additional stabilization.     

Effect of the guest size and shape on its binding dynamics with sodium cholate aggregates

The binding dynamics of the guests acenaphthene, phenanthrene, fluorene, and acenaphthenol with sodium cholate aggregates were studied using laser flash photolysis and fluorescence. The location of the guests in the bile salt aggregate is determined by the guest's hydrophobicity, where acenaphthene, phenanthrene, and fluorene bind to the primary aggregates, while acenaphthenol binds to the secondary bile salt aggregates. The residence time of the guests in the primary aggregates and the access of ionic species from the aqueous phase to the guest in the aggregate depend on the size and the shape of the guest. These results show that bile salt aggregates are adaptable supramolecular host systems.     

Excess proton solvation and delocalization in a hydrophilic pocket of the proton conducting polymer membrane nafion

Solvation properties of the hydrated excess proton are studied in a hydrophilic pocket of Nafion 117 through a series of molecular dynamics simulations. The multistate empirical valence bond (MS-EVB) methodology, which enables the delocalization of the excess proton through the Grotthuss hopping mechanism, was employed for one of the excess protons in the simulation cell. Simulations were performed such that "classical" nondissociable hydronium cations and a single excess proton treated with the MS-EVB methodology were at a concentration ratio of 39:1. Two degrees of hydration of the Nafion polymer electrolyte membrane were simulated, each displaying the same marked difference between the solvation structures of the classical versus MS-EVB treated (Grotthuss shuttling) excess proton species. These differences are attributed to the solvent dynamics needed to transfer the cation between the solvent separated and contact pair positions about the sulfonic acid counterion. The results demonstrate that it is generally impossible to describe the low pH conditions in the hydrophilic domains of Nafion without the explicit treatment of Grotthuss delocalization in the underlying molecular dynamics model for the excess protons.     

Preferential solvation of Brooker's merocyanine in binary solvent mixtures composed of formamides and hydroxylic solvents

The ET polarity values of 4-[(1-methyl-4(1H)-pyridinylidene)-ethylidene]-2,5-cyclohexadien-1-one (Brooker's merocyanine) were collected in mixed-solvent systems comprising a formamide [N,N-dimethylformamide (DMF), N-methylformamide (NMF) or formamide (FA)] and a hydroxylic (water, methanol, ethanol, propan-2-ol or butan-1-ol) solvent. Binary mixtures involving DMF and the other formamides (NMF and FA) as well as NMF and FA were also studied. These data were employed in the investigation of the preferential solvation (PS) of the probe. Each solvent system was analyzed in terms of both solute-solvent and solvent-solvent interactions. These latter interactions were responsible for the synergism observed in many binary mixtures. This synergistic behaviour was observed for DMF-propan-2-ol, DMF-butan-1-ol, FA-methanol, FA-ethanol and for the mixtures of the alcohols with NMF. All data were successfully fitted to a model based on solvent-exchange equilibria, which allowed the separation of the different contributions of the solvent species in the solvation shell of the dye. The results suggest that both hydrogen bonding and solvophobic interactions contribute to the formation of the solvent complexes responsible for the observed synergistic effects in the PS of the dye.     

Preferential solvation of lysozyme by dimethyl sulfoxide in binary solutions of water and dimethyl sulfoxide

To reveal the denaturation mechanism of lysozyme by dimethyl sulfoxide (DMSO), thermal stability of lysozyme and its preferential solvation by DMSO in binary solutions of water and DMSO was studied by differential scanning calorimetry (DSC) and using densities of ternary solutions of water (1), DMSO (2) and lysozyme (3) at 298.15 K. A significant endothermic peak was observed in binary solutions of water and DMSO except for a solution with a mole fraction of DMSO (x ₂) of 0.4. As x ₂ was increased, the thermal denaturation temperature T _m decreased, but significant increases in changes in enthalpy and heat capacity for denaturation, ΔH _cal and ΔC _p, were observed at low x ₂ before decreasing. The obtained amount of preferential solvation of lysozyme by DMSO (∂g ₂/∂g ₃) was about 0.09 g g⁻¹ at low x ₂, indicating that DMSO molecules preferentially solvate lysozyme at low x ₂. In solutions with high x ₂, the amount of preferential solvation (∂g ₂/∂g ₃) decreased to negative values when lysozyme was denatured. These results indicated that DMSO molecules do not interact directly with lysozyme as denaturants such as guanidine hydrochloride and urea do. The DMSO molecules interact indirectly with lysozyme leading to denaturation, probably due to a strong interaction between water and DMSO molecules.     

Preferential solvation and assisted substitution of chloropentaamminecobalt(III) ion in water-dimethyl sulfoxide media

The composition of the solvent cage of chloropentaamminechromium(III) ion was determined in water—dimethyl sulfoxide media using proton NMR line-broadening methods and the approach of Covington and coworkers. The number of solvent molecules in the solvent cage was found to be 10. The stepwise formation constants for the substitution of 10 water molecules by 10 dimethylsulfoxide molecules in this solvent cage were calculated. After the first such substitution each successive substitution becomes 1027 J mol⁻¹ more difficult, exclusive of statistical factors, than the preceding substitution. The solvent cage composition was assumed to apply to the chloropentaamminecobalt(III) ion. Mercury(II)-assisted removal of chloride ion from the latter complex gave [Co(NH₃)₅{OSMe₂}]³⁺/[Co(NH₃)₅(H₂O)]³⁺ product ratios which did not correlate with either the solvent cage composition or the activity ratio of the two solvent components in the bulk phase of the solvent.     

Combined effect of stacking and solvation on the spontaneous mutation in DNA

In DNA, base pairs are involved in two reciprocal interactions: interbase hydrogen bonds and stacking. Furthermore, base pairs also undergo the effects of the external entities present in the biological environment, such as water molecules and cations. In this contribution, the double spontaneous mutation has been studied with hybrid theoretical tools in a DNA-embedded guanine-cytosine model accounting for the impact of the first hydration shell. According to our findings, the combination of the neighboring base pairs and surrounding water molecules plays a crucial role in the double proton transfer. Indeed, as a consequence of these interactions, the double proton transfer (DPT) mechanism is altered: on the one hand, stacking and hydration strongly affect the geometry of base pairs, and, on the other hand, vicinal water molecules may play an active role in the tautomeric equilibrium by catalyzing the proton transfer reaction.     

Structural and thermodynamic investigations on the aggregation and folding of acylphosphatase by molecular dynamics simulations and solvation free energy analysis

Protein engineering method to study the mutation effects on muscle acylphosphatase (AcP) has been actively applied to describe kinetics and thermodynamics associated with AcP aggregation as well as folding processes. Despite the extensive mutation experiments, the molecular origin and the structural motifs for aggregation and folding kinetics as well as thermodynamics of AcP have not been rationalized at the atomic resolution. To this end, we have investigated the mutation effects on the structures and thermodynamics for the aggregation and folding of AcP by using the combination of fully atomistic, explicit-water molecular dynamics simulations, and three-dimensional reference interaction site model theory. The results indicate that the A30G mutant with the fastest experimental aggregation rate displays considerably decreased α1-helical contents as well as disrupted hydrophobic core compared to the wild-type AcP. Increased solvation free energy as well as hydrophobicity upon A30G mutation is achieved due to the dehydration of hydrophilic side chains in the disrupted α1-helix region of A30G. In contrast, the Y91Q mutant with the slowest aggregation rate shows a non-native H-bonding network spanning the mutation site to hydrophobic core and α1-helix region, which rigidifies the native state protein conformation with the enhanced α1-helicity. Furthermore, Y91Q exhibits decreased solvation free energy and hydrophobicity compared to wild type due to more exposed and solvated hydrophilic side chains in the α1-region. On the other hand, the experimentally observed slower folding rates in both mutants are accompanied by decreased helicity in α2-helix upon mutation. We here provide the atomic-level structures and thermodynamic quantities of AcP mutants and rationalize the structural origin for the changes that occur upon introduction of those mutations along the AcP aggregation and folding processes.     

Preferential solvation of indomethacin and naproxen in ethyl acetate + ethanol mixtures according to the IKBI method

The preferential solvation parameters of indomethacin and naproxen in ethyl acetate + ethanol mixtures are derived from their thermodynamic properties by using the inverse Kirkwood–Buff integrals method. It is found that both drugs are sensitive to solvation effects, so the preferential solvation parameter, δx_EA,D, is negative in ethanol-rich and ethyl acetate-rich mixtures but positive in compositions from 0.36 to 0.71 in mole fraction of ethyl acetate. It is conjecturable that in ethanol-rich mixtures, the acidic interaction of ethanol on basic sites of the analgesics plays a relevant role in the solvation. The more solvation by ethyl acetate in mixtures of similar co-solvent compositions could be due to polarity effects. Finally, the slight preference of these compounds for ethanol in ethyl acetate-rich mixtures could be explained as the common participation of basic sites in both solvents and the acidic site of ethanol. Nevertheless, the specific solute–solvent interactions remain unclear.     

Thermodynamics of solvation and solvophobic effect in formamide

Using semi-adiabatic calorimetry, we measured the enthalpies of solution for various low-polar compounds including alkanes, aromatic hydrocarbons and their halogenated derivatives in formamide at temperature of 298 K. For the same compounds, the values of limiting activity coefficients in formamide were determined using GC headspace analysis at 298 K, and Gibbs free energies of solution and solvation were calculated. Based on these data and the available literature values of the Gibbs free energy of solvation in formamide for a number of other low-polar solutes, a study of the solvophobic effect in this solvent is performed, and its resemblance to the hydrophobic effect in aqueous solutions is demonstrated. It is shown that the contribution of the solvophobic effect into the solvation Gibbs free energy in formamide is much higher than that in aliphatic alcohols, but lower than that in water. Like in water, the magnitude of this contribution for different solutes linearly increases with the solute molecular volume. Solvophobic effect also significantly affects the enthalpies of dissolution in formamide, causing them to be more negative in the case of alkanes and more positive in the case of arenes.     

An improved coarse-grained model of solvation and the hydrophobic effect

We present a coarse-grained lattice model of solvation thermodynamics and the hydrophobic effect that implements the ideas of Lum-Chandler-Weeks theory [J. Phys. Chem. B 134, 4570 (1999)] and improves upon previous lattice models based on it. Through comparison with molecular simulation, we show that our model captures the length-scale and curvature dependence of solvation free energies with near-quantitative accuracy and 2-3 orders of magnitude less computational effort, and further, correctly describes the large but rare solvent fluctuations that are involved in dewetting, vapor tube formation, and hydrophobic assembly. Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations.