How ATP suppresses the fibrillation of amyloid peptides: analysis of the free-energy contributions.

Recent experiments have revealed that adenosine triphosphate (ATP) suppresses the fibrillation of amyloid peptides - a process closely linked to neurodegenerative diseases such as Alzheimer's and Parkinson's. Apart from the adsorption of ATP onto amyloid peptides, the molecular understanding is still limited, leaving the underlying mechanism for the fibrillation suppression by ATP largely unclear, especially in regards to the molecular energetics. Here we provide an explanation at the molecular scale by quantifying the free energies using all-atom molecular dynamics simulations. We found that the changes of the free energies due to the addition of ATP lead to a significant equilibrium shift towards monomeric peptides in agreement with experiments. Despite ATP being a highly charged species, the decomposition of the free energies reveals that the van der Waals interactions with the peptide are decisive in determining the relative stabilization of the monomeric state. While the phosphate moiety exhibits strong electrostatic interactions, the compensation by the water solvent results in a minor, overall Coulomb contribution. Our quantitative analysis of the free energies identifies which intermolecular interactions are responsible for the suppression of the amyloid fibril formation by ATP and offers a promising method to analyze the roles of similarly complex cosolvents in aggregation processes.

Self-association as a solubility limiting factor of riboflavin in aqueous media.

Single crystal X-ray diffraction analysis of needle shaped riboflavin (RF) crystals revealed π-stacking of RF's isoalloxazine units (distance: 3.643-3.313 Å) with syn-orientated ribityl chains. In line with this, classical molecular dynamics (MD) (400 ns) using an isobaric-isothermal (NPT) ensemble of eight RF in a water box (〈V〉 ∼ 508.62 nm3, 〈p〉 = 1.11 bar) revealed anti-aligned aggregation of RF in water (COM-distance: 4 Å). Comparing umbrella sampling for the separation of two RF molecules to the separation of two lumichrome molecules, the similar mean potential force for the separation of RF and lumichrome (22.8 kJ mol-1; 24.4 kJ mol-1) proved dispersive interactions as the origin of RF's aggregation. Though stacking of RF is the major water-solubility limiting factor, the conformation of RF's ribityl chain may alter the solubility in water. Both, MD (in water) and COSMO-RS (in water continuum) predicted that conformations of RF with an extended ribityl chain are thermodynamically preferred over any conformations with internal hydrogen bonds between hydroxyl groups and nitrogen/oxygen atoms of the pyrimidine moiety of the flavin ring. Interestingly, COSMO-RS predicted the solubility of the extended conformation to be significantly lower than the latter leading to the very low average solubility of RF. Nuclear Overhauser effect measurements (NOESY) of the structurally related sodium riboflavin 5'-monophosphate (RF-PO4) in deuterium oxide confirmed π-stacking of the isoalloxazine rings. In conformity with the 350 times higher water-solubility of RF-PO4, NOESY also indicated a contorted conformation of the ribityl phosphate chain, whereas, for RF, indications for a contorted chain were not observed.

Solvation of Nanoions in Aqueous Solutions.

In recent years it has been increasingly recognized that different classes of large ions with multiple valency have effects conceptually similar to weakly solvated ions in the Hofmeister series, also labeled by the term chaotropic. The term "superchaotropic effect" has been coined because these effects are much more strongly pronounced for nanometer-sized ions, whose adsorption properties often resemble typical surfactants. Despite this growing interest in these nanometer-sized ions, a simple conceptual extension of the Hofmeister series toward nanoions has not been achieved because an extrapolation of the one-dimensional surface charge density scale does not lead to the superchaotropic regime. In this work, we discuss a generic model that is broadly applicable to ions of nearly spherical shape and thus includes polyoxometalates and boron clusters. We present a qualitative classification scheme in which the ion size appears as a second dimension. Ions of different sizes but the same charge density differ in their bulk solvation free energy. As the ions grow bigger at constant surface charge density, they become more stable in solution, but the adsorption behavior is still governed by the surface charge density. A detailed molecular dynamics simulation study of large ions that is based on a shifted Lennard-Jones potential is presented that supports the presented classification scheme.

Brønsted Acid Catalysis-Controlling the Competition between Monomeric versus Dimeric Reaction Pathways Enhances Stereoselectivities.

Chiral phosphoric acids (CPA) have become a privileged catalyst type in organocatalysis, but the selection of the optimum catalyst is still challenging. So far hidden competing reaction pathways may limit the maximum stereoselectivities and the potential of prediction models. In CPA-catalyzed transfer hydrogenation of imines, we identified for many systems two reaction pathways with inverse stereoselectivity, featuring as active catalyst either one CPA or a hydrogen bond bridged dimer. NMR measurements and DFT calculations revealed the dimeric intermediate and a stronger substrate activation via cooperativity. Both pathways are separable: Low temperatures and high catalysts loadings favor the dimeric pathway (ee up to -98 %), while low temperatures with reduced catalyst loading favor the monomeric pathway and give significantly enhanced ee (92-99 % ee; prior 68-86 % at higher temperatures). Thus, a broad impact is expected on CPA catalysis regarding reaction optimization and prediction.

Short-chain branched sulfosuccinate as a missing link between surfactants and hydrotropes.

Surfactants aggregate in water into micelles, and these micelles incorporate organic substances to solubilize them. Hydrotropes are compounds that increase the solubility of hydrophobic substances in water without this form of aggregation. Decreasing the chain length of the classical surfactant Aerosol OT (AOT) from C8 to C5 results in a molecule with intermediate properties. Molecular dynamics simulations and surface tension measurements are performed on this short chain derivative of AOT. This compound shows high solubility and at the same time progressive weak aggregation. The hydration of head groups hinders significant plunging into a hydrophobic core, which leads to well defined liquid chain nanodomains. The transition to bicontinuous aggregates is in the concentration range of 1 mol L-1. The sulfonate group of the head groups (placed at the water interface of worm-like aggregates) rather than the aggregate-aggregate interaction is responsible for the unusual small angle X-ray scattering pattern.

Hydrogen-Bond-Modulated Nucleofugality of SeIII Species to Enable Photoredox-Catalytic Semipinacol Manifolds.

Chemical bond activations mediated by H-bond interactions involving highly electronegative elements such as nitrogen and oxygen are powerful tactics in modern catalysis research. On the contrary, kindred catalytic regimes in which heavier, less electronegative elements such as selenium engage in H-bond interactions to co-activate C-Se σ-bonds under oxidative conditions are elusive. Traditional strategies to enhance the nucleofugality of selenium residues predicate on the oxidative addition of electrophiles onto SeII -centers, which entails the elimination of the resulting SeIV moieties. Catalytic procedures in which SeIV nucleofuges are substituted rather than eliminated are very rare and, so far, not applicable to carbon-carbon bond formations. In this study, we introduce an unprecedented combination of O-H⋅⋅⋅Se H-bond interactions and single electron oxidation to catalytically generate SeIII nucleofuges that allow for the formation of new C-C σ-bonds by means of a type I semipinacol process in high yields and excellent selectivity.

Extended Hydrogen Bond Networks for Effective Proton-Coupled Electron Transfer (PCET) Reactions: The Unexpected Role of Thiophenol and Its Acidic Channel in Photocatalytic Hydroamidations.

Preorganization and aggregation in photoredox catalysis can significantly affect reactivities or selectivities but are often neglected in synthetic and mechanistic studies, since the averaging effect of flexible ensembles can effectively hide the key activation signatures. In addition, aggregation effects are often overlooked due to highly diluted samples used in many UV studies. One prominent example is Knowles's acceleration effect of thiophenol in proton-coupled electron transfer mediated hydroamidations, for which mainly radical properties were discussed. Here, cooperative reactivity enhancements of thiophenol/disulfide mixtures reveal the importance of H-bond networks. For the first time an in-depth NMR spectroscopic aggregation and H-bond analysis of donor and acceptor combined with MD simulations was performed revealing that thiophenol acts also as an acid. The formed phosphate-H+-phosphate dimers provide an extended H-bond network with amides allowing a productive regeneration of the photocatalyst to become effective. The radical and acidic properties of PhSH were substituted by Ph2S2 and phosphoric acid. This provides a handle for optimization of radical and ionic channels and yields accelerations up to 1 order of magnitude under synthetic conditions. Reaction profiles with different light intensities unveil photogenerated amidyl radical reservoirs lasting over minutes, substantiating the positive effect of the H-bond network prior to radical cyclization. We expect the presented concepts of effective activation via H-bond networks and the reactivity improvement via the separation of ionic and radical channels to be generally applicable in photoredox catalysis. In addition, this study shows that control of aggregates and ensembles will be a key to future photocatalysis.

Location and Conformation of the LKα14 Peptide in Water/Ethanol Mixtures.

It is widely recognized that solvation is one of the major factors determining structure and functionality of proteins and long peptides, however it is a formidable challenge to address it both experimentally and computationally. For this reason, simple peptides are used to study fundamental aspects of solvation. It is well established that alcohols can change the peptide conformation and tuning of the alcohol content in solution can dramatically affect folding and, as a consequence, the function of the peptide. In this work, we focus on the leucine and lysine based LKα14 peptide designed to adopt an α-helical conformation at an apolar-polar interface. We investigate LKα14 peptide's bulk and interfacial behavior in water/ethanol mixtures combining a suite of experimental techniques (namely, circular dichroism and nuclear magnetic resonance spectroscopy for the bulk solution, surface pressure measurements and vibrational sum frequency generation spectroscopy for the air-solution interface) with molecular dynamics simulations. We observe that ethanol highly affects both the peptide location and conformation. At low ethanol content LKα14 lacks a clear secondary structure in bulk and shows a clear preference to reside at the air-solution interface. When the ethanol content in solution increases, the peptide's interfacial affinity is markedly reduced and the peptide approaches a stable α-helical conformation in bulk facilitated by the amphiphilic nature of the ethanol molecules.

Phase separation of binary mixtures induced by soft centrifugal fields.

We use the model system ethanol-dodecane to demonstrate that giant critical fluctuations induced by easily accessible weak centrifugal fields as low as 2000g can be observed above the miscibility gap of a binary liquid mixture. Moreover, several degrees above the phase transition, i.e. in the one-phase region, strong gradients of ethanol concentration occur upon centrifugation. In this case, the standard interpretation of sedimentation equilibrium in the analytical ultracentrifuge (AUC) yields an apparent molar mass of ethanol three orders of magnitude higher than the real value. Notably, these composition gradients have no influence on the distribution gradient of solutes such as dyes like Nile red. The thick opaque interphase formed upon centrifugation does not appear as the commonly observed sharp meniscus, but as a turbidity zone, similar to critical opalescence. This layer is a few millimeters thick and separates two fluids with low compositional gradients. All these effects can be qualitatively understood and explained using the Flory-Huggins solution model coupled to classical density functional theory (DFT). In this domain hetero-phase fluctuations can be triggered by gravity even far from the critical point. Taking into account Jean Perrin's approach to external fields in colloids, a self-consistent definition of the Flory effective volume and an explicit calculation of the total free energy per unit volume is possible.

Arginine-rich cell-penetrating peptides induce membrane multilamellarity and subsequently enter via formation of a fusion pore.

Arginine-rich cell-penetrating peptides do not enter cells by directly passing through a lipid membrane; they instead passively enter vesicles and live cells by inducing membrane multilamellarity and fusion. The molecular picture of this penetration mode, which differs qualitatively from the previously proposed direct mechanism, is provided by molecular dynamics simulations. The kinetics of vesicle agglomeration and fusion by an iconic cell-penetrating peptide-nonaarginine-are documented via real-time fluorescence techniques, while the induction of multilamellar phases in vesicles and live cells is demonstrated by a combination of electron and fluorescence microscopies. This concert of experiments and simulations reveals that the identified passive cell penetration mechanism bears analogy to vesicle fusion induced by calcium ions, indicating that the two processes may share a common mechanistic origin.

Dehydration Determines Hydrotropic Ion Affinity for Zwitterionic Micelles.

Specific ion effects in zwitterionic micelles, especially for anions, are evident in reaction kinetics, zeta potential, and critical micelle concentration measurements. However, anion adsorption to zwitterionic micelles does not produce significant changes in shape, aggregation number, or interfacial hydration. Here we used molecular dynamics simulation of systems containing sulfobetaine zwitterionic micelles of N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (DPS) and nine different salts to explore ion adsorption in terms of group dehydration. Our results, in line with those obtained for cationic micelles, showed that the adsorption degree of anions containing both hydrophobic and hydrophilic portions, i.e., hydrotropes, were correlated with the ion dehydration and were governed mainly by the hydrophobic portion dehydration upon adsorption.

Solubilization power of surfactant-free microemulsions.

Hydrophobe solubilization concepts rely on the shielding of solutes from water in nonpolar domains comprising traditional surfactants. We show how an octanol/ethanol/water surfactant-free microemulsion solvates hydrophobic propane in small octanol/ethanol aggregates similar to traditional micelles. These aggregates have the comparable solvent quality as bulk octanol/ethanol with the same composition.

How to explain microemulsions formed by solvent mixtures without conventional surfactants.

Ternary solutions containing one hydrotrope (such as ethanol) and two immiscible fluids, both being soluble in the hydrotrope at any proportion, show unexpected solubilization power and allow strange but yet unexplained membrane enzyme activity. We study the system ethanol-water-octanol as a simple model of such kinds of ternary solutions. The stability of "detergentless" micelles or microemulsions in such mixtures was proposed in the pioneering works of Barden and coworkers [Smith GD, Donelan CE, Barden RE (1977)J Colloid Interface Sci60(3):488-496 and Keiser BA, Varie D, Barden RE, Holt SL (1979)J Phys Chem83(10):1276-1281] in the 1970s and then, neglected, because no general explanation for the observations was available. Recent direct microstructural evidence by light, X-ray, and neutron scattering using contrast variation reopened the debate. We propose here a general principle for solubilization without conventional surfactants: the balance between hydration force and entropy. This balance explains the stability of microemulsions in homogeneous ternary mixtures based on cosolvents.

Specific Ion Effects on Zwitterionic Micelles Are Independent of Interfacial Hydration Changes.

Zwitterionic micelles adsorb anions and several techniques were used to determine the specificity of this interaction. Although at a lower intensity, this adsorption can be compared to those observed in cationic micelles, which showed that interfacial dehydration is a fundamental property for the geometry and size of micelles. Because there is no information on the interfacial hydration of zwitterionic micelles, we used dielectric relaxation spectroscopy (DRS) together with molecular dynamics (MD) simulations to evaluate the importance of surface dehydration promoted by the binding of anions at the micellar interface (sodium bromide, sodium methanesulfonate, sodium trifluoroacetate, and sodium triflate) in N-dodecyl- N, N-dimethyl-3-ammonio-1-propanesulfonate (DPS) micelles. Our results, showing good agreement between DRS and MD simulations, strongly suggest that specific ion effects on zwitterionic micelles are unrelated to global changes in the interfacial hydration and depend on specific interactions of the headgroups with selected anions.

Pressure increases the ice-like order of water at hydrophobic interfaces.

A common feature of water close to nonpolar particles, at hydrophobic interfaces, and at the surface to its vapor is the signature of ice-like orientated water molecules. By forming ice-like orientations, the number of unsatisfied hydrogen bonds is minimized and thus the energetic penalty is reduced. To what extent these structural motifs correspond to the existence of a real ice layer has been a long-lasting controversial topic, and the view emerges that the solvation layer is only poorly described as being ice. In this work we present new insight into the ice-like conformations of water at a hydrophobic interface by a detailed analysis of molecular dynamics simulations of water at a hydrophobic self-assembled monolayer under pressures from 1 bar up to 10 kbar. We show by analyzing the ice-like order on different length scales that - despite different signatures of ice-like order - the actual density of ice-like structures is negligible at ambient pressure, but significantly grows with increasing pressure contrary to bulk hexagonal ice, which is destabilized by elevated pressure. At 10 kbar, the interfacial water is of significantly ice-like order.

Salt effects in surfactant-free microemulsions.

The weakly associated micellar aggregates found in the so-called "pre-ouzo region" of the surfactant-free microemulsion water/ethanol/1-octanol are sensitive to changes in the system composition and also to the presence of additives like salt. In this work, we study the influence of two salts, sodium iodide and lithium chloride, on aggregates in water/ethanol/1-octanol by molecular dynamics simulations. In both cases, ethanol concentration in the nonpolar phase and at the interface is increased due to a salting out effect on ethanol in the aqueous pseudo-phase. In addition, minor charging of the interface as a consequence of differential adsorption of anions and cations occurs. However, this charge separation is overall weakened by the erratic surface of octanol aggregates, where polar hydroxyl groups and hydrophobic patches are both present. Furthermore, ethanol at the interface shields hydrophobic patches and reduces the preferential adsorption of iodide and lithium.

The Hydrophobic Gap at High Hydrostatic Pressures.

We have gained new insight into the so-called hydrophobic gap, a molecularly thin region of decreased electron density at the interface between water and a solid hydrophobic surface, by X-ray reflectivity experiments and molecular dynamics simulations at different hydrostatic pressures. Pressure variations show that the hydrophobic gap persists up to a pressure of 5 kbar. The electron depletion in the interfacial region strongly decreases with an increase in pressure, indicating that the interfacial region is compressed more strongly than bulk water. The decrease is most significant up to 2 kbar; beyond that, the pressure response of the depletion is less pronounced.

Hydration and self-aggregation of a neutral cosolute from dielectric relaxation spectroscopy and MD simulations: the case of 1,3-dimethylurea.

The influence of the amphiphile 1,3-dimethylurea (1,3-DMU) on the dynamic properties of water was studied using dielectric relaxation spectroscopy. The experiment provided evidence for substantial retardation of water reorientation in the hydration shell of 1,3-DMU, leading to a separate slow-water relaxation in addition to contributions from bulk-like and fast water as well as from the solute. From the amplitudes of the resolved water modes effective hydration numbers were calculated, showing that each 1,3-DMU molecule effectively freezes the reorientation of 1-2 water molecules. Additionally, a significant amount of solvent molecules, decreasing from ∼39 at infinite dilution to ∼3 close to the solubility limit, is retarded by a factor of ∼1.4 to 2.3, depending on concentration. The marked increase of the solute amplitude indicates pronounced parallel dipole alignment between 1,3-DMU and its strongly bound H2O molecules. Molecular dynamics (MD) simulations of selected solutions revealed a notable slowdown of water rotation for those solvent molecules surrounding the methyl groups of 1,3-DMU and strong binding of ∼2H2O by the hydrophilic carbonyl group, corroborating thus the experimental results. Additionally, the simulations revealed 1,3-DMU self-aggregates of substantial lifetime.

Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures.

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures--while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.

High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent.