Molecular origin of the two-step mechanism of gellan aggregation

Among hydrocolloids, gellan is one of the most studied polysaccharides due to its ability to form mechanically stable gels. Despite its long-standing use, the gellan aggregation mechanism is still not understood because of the lack of atomistic information. Here, we fill this gap by developing a new gellan force field. Our simulations offer the first microscopic overview of gellan aggregation, detecting the coil to single-helix transition at dilute conditions and the formation of higher-order aggregates at high concentration through a two-step process: first, the formation of double helices and then their assembly into superstructures. For both steps, we also assess the role of monovalent and divalent cations, complementing simulations with rheology and atomic force microscopy experiments and highlighting the leading role of divalent cations. These results pave the way for future use of gellan-based systems in a variety of applications, from food science to art restoration.

Modeling Solution Behavior of Poly(N-isopropylacrylamide): A Comparison between Water Models

Water is known to play a fundamental role in determining the structure and functionality of macromolecules. The same crucial contribution is also found in the in silico description of polymer aqueous solutions. In this work, we exploit the widely investigated synthetic polymer poly(N-isopropylacrylamide) (PNIPAM) to understand the effect of the adopted water model on its solution behavior and to refine the computational setup. By means of atomistic molecular dynamics simulations, we perform a comparative study of PNIPAM aqueous solution using two advanced water models: TIP4P/2005 and TIP4P/Ice. The conformation and hydration features of an atactic 30-mer at infinite dilution are probed at a range of temperature and pressure suitable to detect the coil-to-globule transition and to map the P–T phase diagram. Although both water models can reproduce the temperature-induced coil-to-globule transition at atmospheric pressure and the polymer hydration enhancement that occurs with increasing pressure, the PNIPAM–TIP4P/Ice solution shows better agreement with experimental findings. This result can be attributed to a stronger interaction of TIP4P/Ice water with both hydrophilic and hydrophobic groups of PNIPAM, as well as to a less favorable contribution of the solvent entropy to the coil-to-globule transition.

Thermoresponsivity of poly(N-isopropylacrylamide) microgels in water-trehalose solution and its relation to protein behavior

HYPOTHESES

Additives are commonly used to tune macromolecular conformational transitions. Among additives, trehalose is an excellent bioprotectant and among responsive polymers, PNIPAM is the most studied material. Nevertheless, their interaction mechanism so far has only been hinted without direct investigation, and, crucially, never elucidated in comparison to proteins. Detailed insights would help understand to what extent PNIPAM microgels can effectively be used as synthetic biomimetic materials, to reproduce and study, at the colloidal scale, isolated protein behavior and its sensitivity to interactions with specific cosolvents or cosolutes.

EXPERIMENTS

The effect of trehalose on the swelling behavior of PNIPAM microgels was monitored by dynamic light scattering; Raman spectroscopy and molecular dynamics simulations were used to explore changes of solvation and dynamics across the swelling-deswelling transition at the molecular scale.

FINDINGS

Strongly hydrated trehalose molecules develop water-mediated interactions with PNIPAM microgels, thereby preserving polymer hydration below and above the transition while drastically inhibiting local motions of the polymer and of its hydration shell. Our study, for the first time, demonstrates that slowdown of dynamics and preferential exclusion are the principal mechanisms governing trehalose effect on PNIPAM microgels, at odds with preferential adsorption of alcohols, but in full analogy with the behavior observed in trehalose-protein systems.

Interaction of Caffeine with Model Lipid Membranes

Caffeine is not only a widely consumed active stimulant, but it is also a model molecule commonly used in pharmaceutical sciences. In this work, by performing quartz-crystal microbalance and neutron reflectometry experiments we investigate the interaction of caffeine molecules with a model lipid membrane. We determined that caffeine molecules are not able to spontaneously partition from an aqueous environment, enriched in caffeine, into a bilayer. Caffeine could be however included in solid-supported lipid bilayers if present with lipids during self-assembly. In this case, thanks to surface-sensitive techniques, we determined that caffeine molecules are preferentially located in the hydrophobic region of the membrane. These results are highly relevant for the development of new drug delivery vectors, as well as for a deeper understanding of the membrane permeation role of purine molecules.

Molecular insights on poly(N-isopropylacrylamide) coil-to-globule transition induced by pressure

By using extensive all-atom molecular dynamics simulations of an atactic linear polymer chain, we provide microscopic insights into poly(N-isopropylacrylamide) (PNIPAM) coil-to-globule transition addressing the roles played by both temperature and pressure. We detect a coil-to-globule transition up to large pressures, showing a reentrant behavior of the critical temperature with increasing pressure in agreement with experimental observations. Furthermore, again confirming the experimental findings, we report the existence at high pressures of a new kind of globular state. It is characterized by a more structured hydration shell that is closer to PNIPAM hydrophobic domains, as compared to the globular state observed at atmospheric pressure. Our results highlight that temperature and pressure induce a PNIPAM coil-to-globule transition through different molecular mechanisms, opening the way for a systematic use of both thermodynamic variables to tune the location of the transition and the properties of the associated swollen/collapsed states.

Atomic scale investigation of the volume phase transition in concentrated PNIPAM microgels

Combining elastic incoherent neutron scattering and differential scanning calorimetry, we investigate the occurrence of the volume phase transition (VPT) in very concentrated poly-(N-isopropyl-acrylamide) (PNIPAM) microgel suspensions, from a polymer weight fraction of 30 wt. % up to dry conditions. Although samples are arrested at the macroscopic scale, atomic degrees of freedom are equilibrated and can be probed in a reproducible way. A clear signature of the VPT is present as a sharp drop in the mean square displacement of PNIPAM hydrogen atoms obtained by neutron scattering. As a function of concentration, the VPT gets smoother as dry conditions are approached, whereas the VPT temperature shows a minimum at about 43 wt. %. This behavior is qualitatively confirmed by calorimetry measurements. Molecular dynamics simulations are employed to complement experimental results and gain further insights into the nature of the VPT, confirming that it involves the formation of an attractive gel state between the microgels. Overall, these results provide evidence that the VPT in PNIPAM-based systems can be detected at different time- and length-scales as well as under overcrowded conditions.

Molecular Dynamics and Neutron Scattering Studies of Potassium Chloride in Aqueous Solution

Neutron diffraction with isotopic substitution (NDIS) experiments were done on both natural abundance potassium and isotopically labeled ⁴¹KCl heavy water solutions to characterize the solvent structuring around the potassium ion in water. Preliminary measurements suggested that the literature value for the coherent neutron scattering length (2.69 fm) for ⁴¹K was significantly in error. This value was remeasured using a neutron powder diffractometer and found to be 2.40 fm. This revision increases significantly the contrast between the natural abundance K and ⁴¹K by about 30% (from 1.0 to 1.3 fm). The experimentally determined structure factor of the potassium ion was then compared to that calculated from molecular dynamics (MD) simulations. Previous neutron scattering measurements of potassium gave a solvation number of 5.5 (see below). In this study, the NDIS and MD results are in good agreement and allowed us to derive a coordination number of 6.1 for water molecules and 0.8 for chloride ions around each K⁺ ion in 4 molal aqueous KCl solution.

Water-Polymer Coupling Induces a Dynamical Transition in Microgels

The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T _d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.

Numerical modelling of non-ionic microgels: an overview

Microgels are complex macromolecules. These colloid-sized polymer networks possess internal degrees of freedom and, depending on the polymer(s) they are made of, can acquire a responsiveness to variations of the environment (temperature, pH, salt concentration, etc.). Besides being valuable for many practical applications, microgels are also extremely important to tackle fundamental physics problems. As a result, these last years have seen a rapid development of protocols for the synthesis of microgels, and more and more research has been devoted to the investigation of their bulk properties. However, from a numerical standpoint the picture is more fragmented, as the inherently multi-scale nature of microgels, whose bulk behaviour crucially depends on the microscopic details, cannot be handled at a single level of coarse-graining. Here we present an overview of the methods and models that have been proposed to describe non-ionic microgels at different length-scales, from the atomistic to the single-particle level. We especially focus on monomer-resolved models, as these have the right level of details to capture the most important properties of microgels, responsiveness and softness. We suggest that these microscopic descriptions, if realistic enough, can be employed as starting points to develop the more coarse-grained representations required to investigate the behaviour of bulk suspensions.

Crowding and conformation interplay on human DNA G-quadruplex by ultraviolet resonant Raman scattering

The G-quadruplex-forming telomeric sequence (TTAGGG)₄TT was investigated by polarized Ultraviolet Resonance Raman Scattering (UVRR) at 266 nm.

Evidence of a low-temperature dynamical transition in concentrated microgels

A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a "protein-like" dynamical transition in nonbiological aqueous environments. To this aim, we exploit the popular colloidal system of poly-N-isopropylacrylamide (PNIPAM) microgels, extending their investigation to unprecedentedly high concentrations. Owing to the heterogeneous architecture of the microgels, water crystallization is avoided in concentrated samples, allowing us to monitor atomic dynamics at low temperatures. By elastic incoherent neutron scattering and molecular dynamics simulations, we find that a dynamical transition occurs at a temperature T _d ~ 250 K, independently from PNIPAM mass fraction. However, the transition is smeared out on approaching dry conditions. The quantitative agreement between experiments and simulations provides evidence that the transition occurs simultaneously for PNIPAM and water dynamics. The similarity of these results with hydrated protein powders suggests that the dynamical transition is a generic feature in complex macromolecular systems, independently from their biological function.

Molecular Dynamics and Neutron Scattering Studies of Mixed Solutions of Caffeine and Pyridine in Water

Insight into the molecular interactions of homotactic and heterotactic association of caffeine and pyridine in aqueous solution is given on the basis of both experimental and simulation studies. Caffeine is about 5 times more soluble in a 3 m aqueous pyridine solution than it is in pure water (an increase from ∼0.1 m to 0.5 m). At this elevated concentration the system becomes suitable for neutron scattering study. Caffeine-pyridine interactions were studied by neutron scattering and molecular dynamics simulations, allowing a detailed characterization of the spatial and orientational structure of the solution. It was found that while pyridine-caffeine interactions are not as strong as caffeine-caffeine interactions, the pyridine-caffeine interactions still significantly disrupted caffeine-caffeine stacking. The alteration of the caffeine-caffeine stacking, occasioned by the presence of pyridine molecules in solution and the consequent formation of heterotactic interactions, leads to the experimentally detected increase in caffeine solubility.

On the molecular origin of the cooperative coil-to-globule transition of poly(N-isopropylacrylamide) in water

The cooperativity of PNIPAM coil-to-globule transition in water arises from the structuring of solvent in proximity to hydrophobic groups.

By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer–water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain.

Myelography Iodinated Contrast Media. 2. Conformational Versatility of Iopamidol in the Solid State

The phenomenon of polymorphism is of great relevance in pharmaceutics, since different polymorphs have different physicochemical properties, e.g., solubility, hence, bioavailability. Coupling diffractometric and spectroscopic experiments with thermodynamic analysis and computational work opens to a methodological approach which provides information on both structure and dynamics in the solid as well as in solution. The present work reports on the conformational changes in crystalline iopamidol, which is characterized by atropisomerism, a phenomenon that influences both the solution properties and the distinct crystal phases. The conformation of iopamidol is discussed for three different crystal phases. In the anhydrous and monohydrate crystal forms, iopamidol molecules display a syn conformation of the long branches stemming out from the triiodobenzene ring, while in the pentahydrate phase the anti conformation is found. IR and Raman spectroscopic studies carried out on the three crystal forms, jointly with quantum chemical computations, revealed that the markedly different spectral features can be specifically attributed to the different molecular conformations. Our results on the conformational versatility of iopamidol in different crystalline phases, linking structural and spectroscopic evidence for the solution state and the solid forms, provide a definite protocol for grasping the signals that can be taken as conformational markers. This is the first step for understanding the crystallization mechanism occurring in supersaturated solution of iopamidol molecules.

Stacking and Branching in Self-Aggregation of Caffeine in Aqueous Solution: From the Supramolecular to Atomic Scale Clustering

The dynamical and structural properties of caffeine solutions at the solubility limit have been investigated as a function of temperature by means of MD simulations, static and dynamic light scattering, and small angle neutron scattering experiments. A clear picture unambiguously supported by both experiment and simulation emerges: caffeine self-aggregation promotes the formation of two distinct types of clusters: linear aggregates of stacked molecules, formed by 2-14 caffeine molecules depending on the thermodynamic conditions and disordered branched aggregates with a size in the range 1000-3000 Å. While the first type of association is well-known to occur under room temperature conditions for both caffeine and other purine systems, such as nucleotides, the presence of the supramolecular aggregates has not been reported previously. MD simulations indicate that branched structures are formed by caffeine molecules in a T-shaped arrangement. An increase of the solubility limit (higher temperature but also higher concentration) broadens the distribution of cluster sizes, promoting the formation of stacked aggregates composed by a larger number of caffeine molecules. Surprisingly, the effect on the branched aggregates is rather limited. Their internal structure and size do not change considerably in the range of solubility limits investigated.

Stacking of purines in water: the role of dipolar interactions in caffeine

Concentration dependence of the NCE and the dephasing time show that caffeine molecules aggregate at 80 °C by planar stacking with a relevant contribution of dipole interactions.

Myelography iodinated contrast media. I. Unraveling the atropisomerism properties in solution

The present work reports a thorough conformational analysis of iodinated contrast media: iomeprol, iopamidol (the world's most utilized contrast agent), and iopromide. Its main aim is the understanding of the complex structural features of these atropisomeric molecules, characterized by the presence of many conformers with hindered rotations, and of the role of atropisomerism in the physicochemical properties of their aqueous solutions. The problem was tackled by using an extensive analysis of (13)C NMR data on the solutions of whole molecules and of simple precursors in addition to FT-IR investigation and molecular simulations. This analysis demonstrated that out of the many possible atropisomers, only a few are significantly populated, and their relative population is provided. The conformational analysis also indicated that the presence of a sterically hindered amidic bond, allowing a significant population of cis forms (E in iopromide and exo in iomeprol), may be the basis for an increased thermodynamic solubility of concentrated solutions of iomeprol.

The Interaction of Sorbitol with Caffeine in Aqueous Solution

Molecular dynamics simulations were carried out on a system of caffeine interacting with the sugar alcohol sorbitol. The system examined had a caffeine concentration 0.083 m and a sugar concentration 1.08 m. The trajectories of all molecules in the system were collected over a period of 80 ns and analyzed to determine whether there is any tendency for sorbitol to bind to caffeine, and if so, by what mechanism. The results show that the sorbitol molecules have an affinity for the caffeine molecules and that the binding occurred by the interaction of the aliphatic hydrophobic protons of the sugar with the caffeine face. This intermolecular association via face-to-face stacking, as suggested by simulation studies, is similar to that found for sucrose and for D-glucose, which overwhelmingly exists in the pyranose ring chair form in aqueous solution, as well as for caffeine-caffeine association. The sorbitol molecules, however, exist as relatively extended chains and are, therefore, topologically quite different from the sugars sucrose and glucose. The comparison of the average conformation of sorbitol molecules bound to caffeine with that of molecules in the free state shows a substantial similarity.

Caffeine and sugars interact in aqueous solutions: a simulation and NMR study

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 m solution of α-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 m solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.

Molecular dynamics simulation studies of caffeine aggregation in aqueous solution

Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.