The impact of force field models on the thermal and mechanical characteristics of polyimides was comprehensively examined for the first time. Polyimides (PI) are heterocyclic polymers with outstanding thermal and chemical stabilities and excellent dielectric properties. In this study, we used all-atom molecular dynamics (MD) simulations to examine how the flexibility of the dianhydride fragment affects the thermal and mechanical properties of three polyimides: PMDA-ODA, ODPA-ODA, and R-ODA. The considered polyimides have different dianhydride fragments based on pyromellitic acid (PMDA), tetracarboxylic acid diphenyl oxide (ODPA) and 1,3-bis(3',4-dicarboxyphenoxy)benzene acid (R), with a constant diamine: 4,4'-oxydianiline (ODA). Models were built using five classical force fields (OPLS-AA, Amber/GAFF, Gromos, Charmm/CGenFF, and UFF). For each polyimide, eight models were generated using different force fields and charge schemes: (i) OPLS-AA with 1.14*CM1A charges, (ii) OPLS-AA with HF/6-31G* (RESP) charges, (iii) GAFF with AM1-BCC charges, (iv) GAFF with HF/6-31G* (RESP) charges, (v) CGenFF (version 4.6) with native charges, (vi) CGenFF (version 5.0) with native charges, (vii) Gromos54a7 with native charges, and (viii) UFF with QEq charges. The difference in the chemical structures of the polyimide repeating unit leads to differences in the thermodynamic and kinetic flexibilities that affect the thermal and mechanical properties. Simulations of glass transition temperatures (Tg) for three polyimides PMDA-ODA, ODPA-ODA, and R-ODA mostly replicate the experimental order Tg(PMDA-ODA) > Tg(ODPA-ODA) > Tg(R-ODA), except for the CGenFF (version 4.6) force field. The experimental density ratio ρ(PMDA-ODA) > ρ(ODPA-ODA) > ρ(R-ODA) is most accurately replicated by OPLS-AA (RESP) and CGenFF (version 5.0) polyimide models. The coefficients of thermal expansion (CTE) correspond with the experimental trend, exhibiting an increase in the following order: PMDA-ODA < ODPA-ODA < R-ODA. Gromos54a7 precisely delineates both the ratio and absolute values CTE for all polymers. OPLS-AA (RESP), OPLS-AA (CM1A), CGenFF (version 4.6), and UFF (QEq) models replicate PMDA-ODA's CTE, while GAFF (RESP) and GAFF (AM1-BCC) models replicate ODPA-ODA and R-ODA CTE values. The ratio between the simulated values of Young's modulus, yield strength, and strain-hardening modulus followed the sequence PMDA-ODA > ODPA-ODA > R-ODA for the OPLS-AA (RESP) and CGenFF (version 5.0) models.

Polymerizable deep eutectic solvents (DES) are promising starting materials for preparation of eutectogels and hydrogels that can be applied in drug delivery, as strain sensors and various components of soft electronics. However, the understanding of relationship between the molecular structure, physicochemical properties and polymerization behavior of such systems in pure state and in their mixtures with water is not well studied yet. In this work we report the results of both computer simulation and experimental investigations for polymerizable choline chloride/acrylic acid DES and its mixtures with water. Molecular dynamics was applied to reveal the influence of water on the structure of polymerizable DES at the molecular and supramolecular levels. The diffusion coefficients of DES components with different water content were measured using NMR. The course of photoinduced polymerization of DES/water mixtures was traced using FTIR spectroscopy, while the molar mass and hydrodynamic characteristics of obtained polyacrylic acid were studied by means of static and dynamic light scattering. It was found that addition of water leads to a gradual decrease in size of the acrylic acid clusters that exist in pure DES and is accompanied by an increase in orientation mobility and diffusion coefficients of components. The maximal molar mass was obtained for the polymer prepared by polymerization of DES with 5 wt% of water. This can be attributed to the optimal combination of acrylic acid clusters size and increased mobility of components.

The aim of this work was to study the influence of water as a co-solvent on the interaction between a polymerizable ionic liquid—choline acrylate (ChA)—and bacterial cellulose. Bacterial cellulose dispersed in ChA is a new type of UV-curable biopolymer-based ink that is a prospective material for the 3D printing of green composite ion-gels. Higher cellulose content in inks is beneficial for the ecological and mechanical properties of materials, and leads to increased viscosity and the yield stress of such systems and hampers printability. It was found that the addition of water results in (1) a decrease in the solvent viscosity and yield stress; and (2) a decrease in the stability of dispersion toward phase separation under stress. In this work, an optimal composition in the range of 30–40 wt% water content demonstrating 97–160 Pa of yield stress was found that ensures the printability and stability of inks. The rheological properties of inks and mechanical characteristics (0.7–0.8 MPa strength and 1.1–1.2 MPa Young’s modulus) were obtained. The mechanism of influence of the ratio ChA/water on the properties of ink was revealed with atomic force microscopy, wide-angle X-ray diffraction studies of bacterial cellulose after regeneration from solvent, and computer simulation of ChA/water mixtures and their interaction with the cellulose surface.

Deep eutectic solvents (DESs) are multi-component solvents appearing in a broad range of applications. The next necessary step for the development of new DESs is understanding the molecular mechanisms of DES formation and the interactions that determine its structure and properties. In this work, we use multiscale simulations supported by experiments to investigate the detailed structure and properties of polymerizable DESs based on choline chloride and acrylic acid as a basis for creating inks for 3D printing. Thermodynamic and structural analyses show the physical mechanisms of DES formation in these materials: due to the significant size difference between the acrylic acid and choline ions, and favorable interactions between acrylic acid and the Cl- ions, the acrylic acid molecules are able to incorporate into the free spaces of the first coordination shells of the Cl- ions. As a consequence, the mixture has less volume than its individual components and this excess volume determines the negative value of the enthalpy of mixing. Structurally, the mixture is a network with the Cl- ions as nodes connecting the other DES components. This was confirmed by both the FTIR experiments and the atomistic MD simulations. The calculations show the necessity of correct accounting of excess enthalpy and entropy for determining DESs structures and other properties.(c) 2022 Elsevier B.V. All rights reserved.

Electrostatic interactions have a determining role in the conformational and dynamic behavior of polyelectrolyte molecules. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in a water solution with the most commonly used K+ or Na+ counterions, were investigated using atomistic molecular dynamics (MD) simulations. We performed a comparison of seven popular force fields, namely AMBER99SB-ILDN, AMBER14SB, AMBER-FB15, CHARMM22*, CHARMM27, CHARMM36m and OPLS-AA/L, both with their native parameters and using two common corrections for overbinding of ions, the non-bonded fix (NBFIX), and electronic continuum corrections (ECC). These corrections were originally introduced to correct for the often-reported problem concerning the overbinding of ions to the charged groups of polyelectrolytes. In this work, a comparison of the simulation results with existing experimental data revealed several differences between the investigated force fields. The data from these simulations and comparisons with previous experimental data were then used to determine the limitations and strengths of these force fields in the context of the structural and dynamic properties of anionic polyamino acids. Physical properties, such as molecular sizes, local structure, and dynamics, were studied using two types of common counterions, namely potassium and sodium. The results show that, in some cases, both the macroion size and dynamics depend strongly on the models (parameters) for the counterions due to strong overbinding of the ions and charged side chain groups. The local structures and dynamics are more sensitive to dihedral angle parameterization, resulting in a preference for defined monomer conformations and the type of correction used. We also provide recommendations based on the results.

Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications, such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can predict and reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.

Publications showing the prospects of combining computer simulation with atomic force microscopy in the study of polymer biological objects and materials for various purposes are analyzed. The problems that arise when these methods are used together are described. Three main directions are presented in which atomic force microscopy is used in conjunction with computer simulation: study of the surface topography of polymer materials; measurement of the force curve of the interaction of the atomic force probe with polymer structures; and determination of the energy of intermolecular interactions.

We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α,L-glutamic acid and α,L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is to search for ways to control properties such as sorption capacity and the structural response of the brush to multivalent salts. For this detailed understanding of the role of side-chain length, the chemical structure and their interplay are required. It was found that in the case of glutamic acid oligomers, the longer side chains facilitate attractive interactions with the cellulose surface, which forces the grafted chains to lie down on the surface. The additional methylene group in the side chain enables side-chain rotation, enhancing this effect. On the other hand, the shorter and more restricted side chains of aspartic acid oligomers prevent attractive interactions to a large degree and push the grafted chains away from the surface. The difference in side-chain length also leads to differences in other properties of the brush in divalent salt solutions. At a low grafting density, the longer side chains of glutamic acid allow the adsorbed cations to be spatially distributed inside the brush resulting in a charge inversion. With an increase in grafting density, the difference in the total charge of the aspartic and glutamine brushes disappears, but new structural features appear. The longer sides allow for ion bridging between the grafted chains and the cellulose surface without a significant change in main-chain conformation. This leads to the brush structure being less sensitive to changes in salt concentration.

Investigation of the effect of CaCl2 salt on conformations of two anionic poly(amino acids) with different side chain lengths, poly-(α-l glutamic acid) (PGA) and poly-(α-l aspartic acid) (PASA), was performed by atomistic molecular dynamics (MD) simulations. The simulations were performed using both unbiased MD and the Hamiltonian replica exchange (HRE) method. The results show that at low CaCl2 concentration adsorption of Ca2+ ions lead to a significant chain size reduction for both PGA and PASA. With the increase in concentration, the chains sizes partially recover due to electrostatic repulsion between the adsorbed Ca2+ ions. Here, the side chain length becomes important. Due to the longer side chain and its ability to distance the charged groups with adsorbed ions from both each other and the backbone, PGA remains longer in the collapsed state as the CaCl2 concentration is increased. The analysis of the distribution of the mineral ions suggests that both poly(amino acids) should induce the formation of mineral with the same structure of the crystal cell.

An environment-friendly method for obtaining cellulose nanocrystals (CNC) using deep eutectic solvents (DES) was developed. Formation of highly crystalline CNC with average particle dimensions 20 × 100 × 700 nm was confirmed with SEM and AFM. Molecular dynamics simulations demonstrated that the hydrogen bond interactions of the cellulose hydroxyl groups with the urea C=O group and with the chloride ions were the key factors of the destruction of MCC particles in the process of solvation. The type of cellulose crystal structure (Iβ) and the high degree of crystallinity (about 80% according to Segal method) were preserved during treatment with DES. The ability of the prepared CNC to act as a reinforcing filler was tested by introduction of them into the chitosan-based films plasticized with DES. It was found that addition of 2 wt% of CNC led to an increase in the strength of the films from 11.4 up to 20.4 MPa with a simultaneous increase in the elongation at break.

Overbinding of ions is a common and well-known problem in classical molecular dynamics simulations. One of its main causes is the absence of electronic polarizability in the force fields. The current approaches for minimizing overbinding typically either retain the original charges and use an ad hoc readjustment of the Lennard-Jones parameters as done in the nonbonded fix (NBFIX) approach or rescale the charges using a theoretical framework. The goal in the latter is to include shielding produced by the missing electronic polarizability as done in the electronic continuum correction (ECC) approach. NBFIX and ECC are the most common corrections, and we compare their performance to the default parameterizations provided by five different commonly used biomolecular force fields, OPLS-AA/L, CHARMM27, CHARMM36m, CHARMM22*, and AMBER99SB-ILDN. As test systems, we use poly-α,l-glutamic and poly-α,l-aspartic amino acid molecules in explicit water together with Na+ and K+ counterions. We demonstrate that the different force fields yield results that are not only quantitatively but also qualitatively different. The resulting structures of the macroions depend strongly on the model for ions. NBFIX corrections alleviate the problem of overbinding, resulting in extended peptides. The ECC corrections depend nontrivially on the original underlying model, and despite being based on a theoretical framework, they cannot always solve the problem.

Cellulose can be phosphorylated to produce organic matrices with highly adsorptive properties for, e.g., biocompatible materials for biomedical applications. We focus on the effects of phosphorylation of surfaces of crystalline nanocellulose and, in particular, on the competitive adsorption of mono- and divalent cations (Na+ and Ca2+) typically contained in mineralizing salt mixtures using all-atom molecular dynamics (MD) simulations. Phosphorylation was applied at 12% and 25% both in water and CaCl2 solutions. Our main result shows that Na+ and Ca2+ cations are concentrated in different interfacial layers with Na+ ions penetrating much closer to the surface. This behavior cannot be described by the Poisson-Boltzmann theory or implicit solvent simulations. Our analysis shows that the physical origin of this observation is due to a balance between the electrostatic interactions and hydration free energy associated with the ions. Adsorption levels of the different ions also respond differently to changes in the degree of phosphorylation. We show that the number of adsorbed Na+ ions per phosphate group increases whereas the number of adsorbed Ca2+ ions decreases with an increasing degree of phosphorylation (or when the number of binding sites increases). The decrease in the number of adsorbed Ca2+ ions can be explained by an increasing "charge-charge" repulsion between the Ca2+ ions attracted by the charged surface. Importantly, our results demonstrate the existence of an optimum degree of phosphorylation in terms of adsorbed Ca2+ ions and can be used as a guideline in materials design, for example, when choosing the cellulose matrix or with other similarly structured biomolecular and polymer surfaces.

We present results from all-atom molecular dynamics simulations for the structural properties of oligomeric lactic acid chains (OLA) grafted to the surface of cellulose nanocrystals (CNCs) and immersed in the melt of polylactic acid (PLA). Earlier, we have found that the distribution of free ends of OLA molecules is bimodal [Glova et al., Polym. Int., 2016, 65(8), 892]. The results cannot be explained within the standard picture of uncharged polymer brushes exposed to the melt of a chemically identical polymer. Although the oligomeric brushes of the OLA chains are uncharged, they have partial polarization charges producing a non-zero dipole moment of the monomeric chain unit. We study the influence of partial charges on the structure of the layer of OLA chains grafted to the CNC surface. A detailed analysis of the conformations of the grafted chains shows that interaction of partial charges in the models causes bending of the OLA molecules toward the cellulose surface, forming a hairpin structure. The observed separation of the grafted chains into two populations increases with grafting density. We demonstrate that hydrogen bonds can be formed between the free ends of the grafted chains and the CNC surface, but they do not affect the brush structure significantly. Thus, dipole-dipole interactions turn out to be the key factor governing the unusual conformations of grafts.

Specific intermolecular interactions, in particular H-bonding, have a strong influence on the structural, thermal and relaxation characteristics of polymers. We report here the results of molecular dynamics simulations of Nylon 6 which provides an excellent example for the investigation of such an influence. To demonstrate the effect of proper accounting for H-bonding on bulk polymer properties, the AMBER99sb force field is used with two different parametrization approaches leading to two different sets of partial atomic charges. The simulations allowed the study of the thermal and dielectric properties in a wide range of temperatures and cooling rates. The feasibility of the use of the three methods for the estimation of the glass transition temperature not only from the temperature dependence of structural characteristics such as density, but also by using the electrostatic energy and dielectric constant is demonstrated. The values of glass transition temperatures obtained at different cooling rates are practically the same for the three methods. By proper accounting for partial charges in the simulations, a reasonable agreement between the results of our simulations and experimental data for the density, thermal expansion coefficient, static dielectric constant and activation energy of γ and β relaxations is obtained demonstrating the validity of the modeling approach reported.

Molecular-level insight into the interactions of phospholipid molecules with cellulose is crucial for the development of novel cellulose-based materials for wound dressing. Here we employ the state-of-the-art computer simulations to unlock for the first time the molecular mechanisms behind such interactions. To this end, we performed a series of atomic-scale molecular dynamics simulations of phospholipid bilayers on a crystalline cellulose support at various hydration levels of the bilayer leaflets next to the cellulose surface. Our findings clearly demonstrate the existence of strong interactions between polar lipid head groups and the hydrophilic surface of a cellulose crystal. We identified two major types of interactions between phospholipid molecules and cellulose chains: (i) direct attractive interactions between lipid choline groups and oxygens of hydroxyl (hydroxymethyl) groups of cellulose and (ii) hydrogen bonding between phosphate groups of lipids and cellulose's hydroxymethyl/hydroxyl groups. When the hydration level of the interfacial bilayer/support region is low, these interactions lead to a pronounced asymmetry in the properties of the opposite bilayer leaflets. In particular, the mass density profiles of the proximal leaflets are split into two peaks and lipid head groups become more horizontally oriented with respect to the bilayer surface. Furthermore, the lateral mobility of lipids in the leaflets next to the cellulose surface is found to slow down considerably. Most of these cellulose-induced effects are likely due to hydrogen bonding between lipid phosphate groups and hydroxymethyl/hydroxyl groups of cellulose: the lipid phosphate groups are pulled toward the water/lipid interface due to the formation of hydrogen bonds. Overall, our findings shed light on the molecular details of the interactions between phospholipid bilayers and cellulose nanocrystals and can be used for identifying possible strategies for improving the properties of cellulose-based dressing materials via, e.g., chemical modification of their surface.

Polymer bio-nanocomposites are widely used nowadays in various applications. One of the most promising polymers for producing such materials is poly(lactic acid) (PLA) filled with cellulose nanocrystals (CNCs). To increase the compatibility of hydrophobic PLA and hydrophilic cellulose, the surface of the latter can be chemically modified. Among the various surface modifications, the grafting of lactic acid oligomers (OLAs) is of special interest. In this paper, the first all-atom molecular dynamics simulation of nanocomposites of PLA filled with CNCs with surface-grafted OLAs is presented. The influence of the degree of modification of the CNCs with OLA chains on the PLA structure near the CNC surface and on the grafted OLA, as well as on the thermal and mechanical properties of the nanocomposites is studied. It is demonstrated that a 50% modification of CNCs with OLA chains leads to PLA expulsion from the CNC surface. (c) 2016 Society of Chemical Industry

Computer simulations based on all-atom models can provide significant assistance to researchers in understanding molecular mechanisms that lead to the appearance of new properties in composites different than those of the individual components. Recently, this simulation of polymer nanocomposites has become more popular, since it provides answers that cannot be obtained experimentally. To date, there have been only a few publications devoted to the computer simulations of polymer nanocomposites based on cellulose, even though these materials are very promising and attract great attention because of their renewable character. One of the main biodegradable polymers, obtained from natural sources and used for developing such biocomposites, is polylactide (PLA). This chapter focuses on computer simulations of PLA and nanocellulose, as well as on composite materials based on these materials.