Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability.

Understanding the mechanisms influencing poly(ethylene terephthalate) (PET) biodegradation is crucial for developing innovative strategies to accelerate the breakdown of this persistent plastic. In this study, we employed all-atom molecular dynamics simulation to investigate the adsorption process of the LCC-ICCG cutinase enzyme onto the PET surface. Our results revealed that hydrophobic, π-π, and H bond interactions, specifically involving aliphatic, aromatic, and polar uncharged amino acids, were the primary driving forces for the adsorption of the cutinase enzyme onto PET. Additionally, we observed a negligible change in the enzyme's tertiary structure during the interaction with PET (RMSD = 1.35 Å), while its secondary structures remained remarkably stable. Quantitative analysis further demonstrated that there is about a 24% decrease in the number of enzyme-water hydrogen bonds upon adsorption onto the PET surface. The significance of this study lies in unraveling the molecular intricacies of the adsorption process, providing valuable insights into the initial steps of enzymatic PET degradation.

Importance of the Electrostatic Correlations in Surface Tension of Hydrated Reline Deep Eutectic Solvent from Combined Experiments and Molecular Dynamics Simulations.

In this study, the surface tension and the structure of hydrated reline are investigated by using diverse methods. Initially, the surface tension displays a nonlinear pattern as water content increases, decreasing until reaching 45 wt %, then gradually matching that of pure water. This fluctuation is associated with strong electrostatic correlations present in pure reline, which decrease as more water is added. Changes in surface tension reflect a shift from charge layering in pure reline to an increased interfacial hydrogen bonding as the water content rises. This shift causes the segregation of urea molecules into the bulk phase and a gradual anchoring of water molecules to the air-reline interface. An interesting observation is the antisurfactant effect, where heightened interfacial anchoring results in an unexpected increase in real contribution of surface tension. This, along with weakened electrostatic correlations beyond 45 wt % due to reinforced interfacial hydrogen bonding, contributes to the complex behavior of surface tension observed in this study.

Autohesion Mechanisms at Interfaces Between Random Copolymer Melts: Mesoscopic Simulations with Realistic Coarse-Grained Models.

The increasing of welding time during the interdiffusion of a pair of non reacting random copolymer melts favors the strength rate of healing at the interface. Furthermore, the diffusion kinetic during the interpenetration of copolymer chains across the interface is strongly dependant on molecular weight. In this paper we perform mesoscopic simulations with realistic coarse grain models to study the autohesion mechanism across the interface between slightly entangled styrene-butadiene random copolymer melts.

Development of anisotropic force fields for homopolymer melts at the mesoscale.

With the aim of producing realistic coarse-grained models of homopolymers, we introduce a tabulated backbone-oriented anisotropic potential. The parameters of the model are optimized using statistical trajectory matching. The impact of grain anisotropy is evaluated at different coarse-graining levels using cis-polybutadiene as a test case. We show that, at the same time, tuning the aspect ratio of the grains can lead to a better density and structure and may reduce the unphysical bond crossings by up to 90%, without increasing the computation time too much and thereby jeopardizing the main advantage of coarse-grained models.

Photodegradation of Triclosan on the Kaolinite Surface: Kinetic, Mechanistic, and Molecular Modeling Approach.

The photodegradation of triclosan (TCS) was investigated on the kaolinite surface. The quantum yield was evaluated, and the photoproducts were identified by HPLC/MS (LC/Q-TOF), showing that the phototransformation is completely different from that reported in aqueous solutions. In particular, the formation of dioxin derivatives was fostered and occurred with a higher efficiency when compared to aqueous solutions. This suggests that TCS has specific interactions with the clay that clearly modifies its photochemical behavior. Moreover, it has also been shown that higher concentrations of TCS, namely, higher than 1.0 µmol g-1 of kaolinite, lead to a significant decrease of the photodegradation rate constant and enhance the formation yield of dimer-type photoproducts. This suggests that the distribution of TCS is clearly not homogeneous at the clay surface and the formation of aggregates is more likely occurring. To get a better insight into this specific interaction, a molecular dynamic modeling of TCS adsorption at the surface of kaolinite was carried out. This clearly shows that when equilibrium is reached, TCS binds to the kaolinite surface by hydrogen bonds involving the phenol function of TCS and the hydroxyl groups of the kaolinite surface. Such behavior confers a particular conformation to the adsorbed TCS that is different from that obtained in water and which could be a key step to partially explain the specific photochemical reactivity in both media. In addition, several TCS molecules appear to interact with each other through the π-stacking (aromatic stacking) process while retaining this hydrogen bond with the kaolinite surface. This is clearly in favor of cluster formation on the clay surface and promotes dimer-type photoproducts.

A Consistent Thermodynamic Characterization of the Adsorption Process through the Calculation of Free Energy Contributions.

We apply in this study different methodologies based on thermodynamic integration (TI), free energy perturbation (FEP), and potential of mean force (PMF) to address the challenging issue of the calculation of the free energy of adsorption. A model system composed of a solid substrate, an adsorbate, and solvent particles is specifically designed to reduce the dependence of our free energy results on the sampling of the phase space and the choice of the pathway. The reliability and efficiency of these alchemical free energy simulations are established through the closure of a thermodynamic cycle describing the adsorption process in solution and in a vacuum. We complete this study by the calculation of free energy contributions related to phenomena of desorption of solvent molecules and desolvation of the adsorbate upon adsorption. This calculation relies on the work of adhesion, the interfacial tension of the liquid-vapor of the solvent, and the free energy of solvation of the substrate. The different ways of calculating the free energy of adsorption are in excellent agreement and could complete experiments in the field of adsorption by giving quantitative data on the different energy contributions involved in the process.

Energetic and Structural Characterizations of the PET-Water Interface as a Key Step in Understanding Its Depolymerization.

We report molecular simulations of the interaction between poly(ethylene terephthalate) (PET) surfaces and water molecules with a short-term goal to better evaluate the different energy contributions governing the enzymatic degradation of amorphous PET. After checking that the glass transition temperature, density, entanglement mass, and mechanical properties of an amorphous PET are well reproduced by our molecular model, we extend the study to the extraction of a monomer from the bulk surface in different environments, i.e., water, vacuum, dodecane, and ethylene glycol. We complete this energetic characterization by the calculation of the work of adhesion of PET surfaces with water and dodecane molecules and by the determination of the contact angle of water droplets. These calculations are compared with experiments and should help us to better understand the enzymatic degradation of PET from both the thermodynamic and molecular viewpoints.

Impact of the Force Field on the Calculation of Density and Surface Tension of Epoxy-Resins.

The molecular simulation of interfacial systems is a matter of debate because of the choice of many input parameters that can affect significantly the performance of the force field of reproducing the surface tension and the coexisting densities. After developing a robust methodology for the calculation of the surface tension on a Lennard-Jones fluid, we apply it with different force fields to calculate the density and surface tension of pure constituents of epoxy resins. By using the model that best reproduces the experimental density and surface tension, we investigate the impact of composition in mass fraction on uncured epoxy resins and the effects of degree of cross-linking on cured resins.

Molecular Simulations of Thermomechanical Properties of Epoxy-Amine Resins.

All-atom molecular dynamics (MD) simulations were performed with the CHARMM force field to characterize various epoxy resins, such as aliphatic and bisphenol-based resins. A multistep cross-linking algorithm was established, and key properties such as density, glass temperature, and elastic modulus were calculated. A quantitative comparison was made and was proven to be in good agreement with experimental data, with average absolute deviations between experiments and molecular simulation comprised between 2% and 12%. Additional findings on structure-property relationships were highlighted such as the effect of the cross-linking rate and oligomerization of the resin.

Investigation of the Complexation between 4-Aminoazobenzene and Cucurbit[7]uril through a Combined Spectroscopic, Nuclear Magnetic Resonance, and Molecular Simulation Studies.

Cucurbiturils are well known for their ability to form supramolecular systems with ultrahigh affinities binding. Inclusion complex between 4-aminoazobenzene and cucurbit[7]uril has been investigated in aqueous solution by ultraviolet (UV)-spectroscopy, 1H NMR, and molecular simulations. 4-aminoazobenzene shows high affinity in acidic solutions while no association was detected in neutral solutions. The thermodynamic properties of complex formation are investigated using both UV spectroscopy and nuclear magnetic resonance (NMR) measurements. Our results highlight that the high binding constant between CB7 and 4AA (log K = 4.9) is the result of a large negative change in Δr H° (-19 kJ/mol) and a small positive change in TΔr S° (9 kJ/mol). The analysis of the experimental data lead to hypothesis on the structure of the complex. We have used molecular dynamics simulation to interpret experiments. Interestingly, the cis-trans isomerization of aminoazobenzene is considered. All the results are discussed and compared with those previously obtained with other host molecules.

Molecular interactions at the metal-liquid interfaces.

We reported molecular simulations of the interactions among water, an epoxy prepolymer diglycidic ether of bisphenol A (DGEBA), and a hardener isophorone diamine (IPDA) on an aluminum surface. This work proposes a comprehensive thermodynamic characterization of the adhesion process from the calculation of different interfacial tensions. The cross-interactions between the atoms of the metal surface and different molecules are adjusted so as to reproduce the experimental work of adhesion. Water nanodroplets on the metal surface are then simulated to predict their contact angle. Liquid-vapor surface tensions of the epoxy prepolymer (DGEBA) and hardener (IPDA) and the solid-vapor surface tension of the aluminum surface are also calculated to provide the solid-liquid interfacial tension that remains very difficult to obtain from the mechanical definition.

Insulin Adsorption onto PE and PVC Tubings.

We investigate the adsorption of insulin onto PE and PVC materials by using HPLC measurements and computer simulations. We interpret the experiments by calculating the Gibbs free energy profiles during the adsorption process. The values of free energy of adsorption show a good agreement with the experimental measurements. The adsorption of insulin onto the different materials is characterized through the conformational changes with respect to its conformation in water and the interfacial regions, which are described by specific arrangements of polymer chains, water, insulin, and plasticizer molecules.

Enhancing the Thermostability of Engineered Laccases in Aqueous Betaine-Based Natural Deep Eutectic Solvents.

In recent years, natural deep eutectic solvents (NADESs) have gained increasing attention as promising nontoxic solvents for biotechnological applications, due to their compatibility with enzymes and ability to enhance their activity. Betaine-based NADESs at a concentration of 25 wt % in a buffered aqueous solution were used as media to inhibit thermal inactivation of POXA1b laccase and its five variants when incubated at 70 and 90 °C. All the tested laccases showed higher residual activity when incubated in NADES solutions, with a further enhancement achieved also for the most thermostable variant. Furthermore, the residual activity of laccases in the presence of NADESs showed a clear advantage over the use of NADESs' individual components. Molecular docking simulations were performed to understand the role of NADESs in the stabilization of laccases toward thermal inactivation, evaluating the interaction between each enzyme and NADESs' individual components. A correlation within the binding energies between laccases and NADES components and the stabilization of the enzymes was demonstrated. These findings establish the possibility of preincubating enzymes in NADESs as a facile and cost-effective solution to inhibit thermal inactivation of enzymes when exposed to high temperatures. This computer-aided approach can assist the tailoring of NADES composition for every enzyme of interest.

Rheological properties of polymer chains at a copper oxide surface: Impact of the chain length, surface coverage, and grafted polymer shape.

We employ a recently derived semirealistic set of coarse-grained interactions to simulate polymer brushes of cis-1,4-polybutadiene grafted on a cuprous-oxide surface within the framework of dissipative particle dynamics. We consider two types of brushes, I and Y, that differ in the way they are connected to the surface. Our model explores the impact of free polymer chain length, grafting density of the brush, and imposed shear rate on the structural and dynamic properties of complex metal oxide polymer interfaces.

Strain induced crystallization of polymers at and above the crystallization temperature by coarse-grained simulations.

We examine the behavior of short and long polymers by means of coarse-grained computer simulations of a by-polyvinyl alcohol inspired model. In particular, we focus on the structural changes in the monomer and polymer scales during cooling and the application of uni-axial true strain. The straining of long polymers results in the formation of a semi-crystalline system at temperatures well above the crystallization temperature, which allows for the study of strain induced crystallization.

Understanding and Characterizing the Drug Sorption to PVC and PE Materials.

Characterizing the sorption of drugs onto polyvinylchloride (PVC) and polyethylene (PE) materials in terms of thermodynamic adsorption properties and atomistic details (local arrangements, orientation, and diffusion) is fundamental for the development of alternative materials that would limit drug sorption phenomena and plasticizer release. Here, a combination of experiments and sophisticated calculations of potential of mean forces are carried out to investigate the sorption of paracetamol and diazepam to PE and PVC surfaces. The simulated Gibbs free energies of adsorption are in line with the experimental interpretations. The polymer-drug-water interface is then characterized at the molecular scale by an in-depth investigation of local properties such as density, orientation, and diffusion.

Assessing the derivation of time parameters from branched polymer coarse-grain model.

The parameterization of rheological models for polymers is often obtained from experiments via the top-down approach. This procedure allows us to determine good fitting parameters for homogeneous materials but is less effective for polymer mixtures. From a molecular simulation point of view, the timescales needed to derive those parameters are often accessed through the use of coarse-grain potentials. However, these potentials are often derived from linear model systems and the transferability to a more complex structure is not straightforward. Here, we verify the transferability of a potential computed from linear polymer simulations to more complex molecular shapes and present a type of analysis, which was recently formulated in the framework of a tube theory, to a coarse-grain molecular approach in order to derive the input parameters for a rheological model. We describe the different behaviors arising from the local topological structure of molecular sub-units. Coarse-grain models and mean-field based tube theory for polymers form a powerful combination with potentially important applications.

Heterogeneity Effects in Highly Cross-Linked Polymer Networks.

Despite their level of refinement, micro-mechanical, stretch-based and invariant-based models, still fail to capture and describe all aspects of the mechanical properties of polymer networks for which they were developed. This is for an important part caused by the way the microscopic inhomogeneities are treated. The Elastic Network Model (ENM) approach of reintroducing the spatial resolution by considering the network at the level of its topological constraints, is able to predict the macroscopic properties of polymer networks up to the point of failure. We here demonstrate the ability of ENM to highlight the effects of topology and structure on the mechanical properties of polymer networks for which the heterogeneity is characterised by spatial and topological order parameters. We quantify the macro- and microscopic effects on forces and stress caused by introducing and increasing the heterogeneity of the network. We find that significant differences in the mechanical responses arise between networks with a similar topology but different spatial structure at the time of the reticulation, whereas the dispersion of the cross-link valency has a negligible impact.

Associated molecular liquids at the graphene monolayer interface.

We report molecular simulations of the interaction between a graphene sheet and different liquids such as water, ethanol, and ethylene glycol. We describe the structural arrangements at the graphene interface in terms of density profiles, number of hydrogen bonds (HBs), and local structuration in neighboring layers close to the surface. We establish the formation of a two-dimensional HB network in the layer closest to the graphene. We also calculate the interfacial tension of liquids with a graphene monolayer and its profile along the direction normal to the graphene to rationalize and quantify the strengthening of the intermolecular interactions in the liquid due to the presence of the surface.

Backbone oriented anisotropic coarse grains for efficient simulations of polymers.

Despite the fact that anisotropic particles have been introduced to describe molecular interactions for decades, they have been poorly used for polymers because of their computing time overhead and the absence of a relevant proof of their impact in this field. We first report a method using anisotropic beads for polymers, which solves the computing time issue by considering that beads keep their principal orientation alongside the mean local backbone vector of the polymer chain, avoiding the computation of torques during the dynamics. Applying this method to a polymer bulk, we study the effect of anisotropic interactions vs isotropic ones for various properties such as density, pressure, topology of the chain network, local structure, and orientational order. We show that for different classes of potentials traditionally used in molecular simulations, those backbone oriented anisotropic beads can solve numerous issues usually encountered with isotropic interactions. We conclude that the use of backbone oriented anisotropic beads is a promising approach for the development of realistic coarse-grained potentials for polymers.