Force Field-based Molecular Dynamics Simulations Research Articles

Effects of graphene reinforcement on morphology, thermophysical, and mechanical properties of polyvinyl alcohol and polyacrylamide in condensed phases

The subtle interplay of noncovalent interaction in enhancing the compatibility between the graphene-based material and the oligomers of polyvinyl alcohol (PVA) and polyacrylamide (PAM) in the solvent phase is unraveled within the framework of all-atom classical force field-based molecular dynamics (MD) simulations. The decomposition of binding free energy analysis demonstrates that the interaction between polymer segments and graphene (G)-surface crucially emanates from the van der Waals (vdW) interactions, while the adsorption of polymer chains on the graphene oxide (GO)-surface is influenced by vdW and electrostatic interactions. The influence of diverse factors including the strain rate, the size of the nanofiller, the number of oligomers, and the thermal quenching rate on controlling the morphology, mechanical, and thermophysical properties of the graphene-reinforced polymer nanocomposites are further explored. The uniaxial deformation simulations of the graphene-reinforced PVA and PAM matrices show that the interfacial mechanical strength is escalated for the G-PVA nanocomposite. The inclusion of graphene nanofiller reduces the polymer chain mobility and increases the intermolecular interaction, which in turn enhances the toughness of the graphene-polymer composites. Increasing the strain rate raises the yield strength and modulus, making the composites appear stronger and stiffer. As evidenced by the predicted glass transition temperature, the thermal stability of the PVA and PAM matrices is significantly improved by the graphene reinforcement.

Correlating Substrate Reactivity at Electrified Interfaces with the Electrolyte Structure in Synthetically Relevant Organic Solvent/Water Mixtures.

Optimizing electrosynthetic reactions requires fine tuning of a vast chemical space, including charge transfer at electrocatalyst/electrode surfaces, engineering of mass transport limitations, and complex interactions of reactants and products with their environment. Hybrid electrolytes, in which supporting salt ions and substrates are dissolved in a binary mixture of organic solvent and water, represent a new piece of this complex puzzle as they offer a unique opportunity to harness water as the oxygen or proton source in electrosynthesis. In this work, we demonstrate that modulating water-organic solvent interactions drastically impacts the solvation properties of hybrid electrolytes. Combining various spectroscopies with synchrotron small-angle X-ray scattering (SAXS) and force field-based molecular dynamics (MD) simulations, we show that the size and composition of aqueous domains forming in hybrid electrolytes can be controlled. We demonstrate that water is more reactive for the hydrogen evolution reaction (HER) in aqueous domains than when strongly interacting with solvent molecules, which originates from a change in reaction kinetics rather than a thermodynamic effect. We exemplify novel opportunities arising from this new knowledge for optimizing electrosynthetic reactions in hybrid electrolytes. For reactions proceeding first via the activation of water, fine tuning of aqueous domains impacts the kinetics and potentially the selectivity of the reaction. Instead, for organic substrates reacting prior to water, aqueous domains have no impact on the reaction kinetics, while selectivity may be affected. We believe that such a fine comprehension of solvation properties of hybrid electrolytes can be transposed to numerous electrosynthetic reactions.

Free Energy Landscapes of the Tautomeric Interconversion of Pyridoxal 5'-Phosphate Aldimines at the Active Site of Ornithine Decarboxylase in Aqueous Media.

The pyridoxal 5'-phosphate (PLP) acts as a coenzyme for a large number of biochemical reactions. It exists in mainly two bound forms at the active site of the concerned enzyme: the internal aldimine, in which the PLP is bound with the ϵ-amino group of lysine at the active site, and the external aldimine, where the PLP is bound to the substrate amino acid. Both the internal and external aldimines have Schiff base linkage (N-H-O) and can exist in two tautomeric structures of ketoenamine and enolimine forms. In this work, we have investigated the free energy landscape for the tautomeric proton transfer in the internal and external aldimines at the active site of the ornithine decarboxylase enzyme in an aqueous medium. We performed hybrid quantum-classical metadynamics and force field-based molecular dynamics simulations, which revealed that the ketoenamine tautomer is more stable than the enolimine form. The QM/MM metadynamics calculations show that the free energy difference between the ketoenamine and enolimine forms for the internal aldimine is 3.9 kcal/mol, and it is found to be 5.8 kcal/mol for the external aldimine, with the ketoenamine form being more stable in both cases. The results are further supported by calculations of the binding free energies from classical simulations and static quantum chemical calculations in different environments. We have also analyzed the configurational structure of the microenvironment at the active site in order to have better insights into the interactions of the active site residues with the PLP in its two tautomeric forms.

Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism.

To combat mischievous coronavirus disease followed by continuous upgrading of therapeutic strategy against the antibody-resistant variants, the molecular mechanistic understanding of protein-drug interactions is a prerequisite in the context of target-specific rational drug development. Herein, we attempt to decipher the structural basis for the inhibition of SARS-CoV-2 main protease (Mpro) through the elemental analysis of potential energy landscape and the associated thermodynamic and kinetic properties of the enzyme-inhibitor complexes using automated molecular docking calculations in conjunction with classical force field-based molecular dynamics (MD) simulations. The crux of the scalable all-atom MD simulations consummated in explicit solvent media is to capture the structural plasticity of the viral enzyme due to the binding of remdesivir analogues and ascertain the subtle interplay of noncovalent interactions in stabilizing specific conformational states of the receptor that controls the biomolecular processes related to the ligand binding and dissociation kinetics. To unravel the critical role of modulation of the ligand scaffold, we place further emphasis on the estimation of binding free energy as well as the energy decomposition analysis by employing the generalized Born and Poisson-Boltzmann models. The estimated binding affinities are found to vary between -25.5 and -61.2 kcal/mol. Furthermore, the augmentation of inhibitory efficacy of the remdesivir analogue crucially stems from the van der Waals interactions with the active site residues of the protease. The polar solvation energy contributes unfavorably to the binding free energy and annihilates the contribution of electrostatic interactions as derived from the molecular mechanical energies.

Interfacial Tensions, Solubilities, and Transport Properties of the H2/H2O/NaCl System: A Molecular Simulation Study.

Data for several key thermodynamic and transport properties needed for technologies using hydrogen (H2), such as underground H2 storage and H2O electrolysis are scarce or completely missing. Force field-based Molecular Dynamics (MD) and Continuous Fractional Component Monte Carlo (CFCMC) simulations are carried out in this work to cover this gap. Extensive new data sets are provided for (a) interfacial tensions of H2 gas in contact with aqueous NaCl solutions for temperatures of (298 to 523) K, pressures of (1 to 600) bar, and molalities of (0 to 6) mol NaCl/kg H2O, (b) self-diffusivities of infinitely diluted H2 in aqueous NaCl solutions for temperatures of (298 to 723) K, pressures of (1 to 1000) bar, and molalities of (0 to 6) mol NaCl/kg H2O, and (c) solubilities of H2 in aqueous NaCl solutions for temperatures of (298 to 363) K, pressures of (1 to 1000) bar, and molalities of (0 to 6) mol NaCl/kg H2O. The force fields used are the TIP4P/2005 for H2O, the Madrid-2019 and the Madrid-Transport for NaCl, and the Vrabec and Marx for H2. Excellent agreement between the simulation results and available experimental data is found with average deviations lower than 10%.

Exploring the adsorption behavior of molecular hydrogen on CHA-zeolite by comparing the performance of various force field methods.

Molecular hydrogen (H2) adsorption plays a crucial role in numerous applications, including hydrogen storage and purification processes. Understanding the interaction of H2 with porous materials is essential for designing efficient adsorption systems. In this study, we investigate H2 adsorption on CHA-zeolite using a combination of density functional theory (DFT) and force field-based molecular dynamics (MD) simulations. Firstly, we employ DFT calculations to explore the energetic properties and adsorption sites of H2 on the CHA-zeolite framework. The electronic structure and binding energies of H2 in various adsorption configurations are analyzed, providing valuable insights into the nature of the adsorption process. Subsequently, force field methods are employed to perform extensive MD simulations, allowing us to study the dynamic behavior of H2 molecules adsorbed on the CHA-zeolite surface. The trajectory analysis provides information on the diffusion mechanisms and mobility of H2 within the porous structure, shedding light on the transport properties of the adsorbed gas. Furthermore, the combination of DFT and MD results enables us to validate and refine the force field parameters used in simulations, improving the accuracy of the model, and enhancing our understanding of the H2-CHA interactions. Our comprehensive investigation into molecular hydrogen adsorption on CHA-zeolite using density functional theory and molecular dynamics simulations yields valuable insights into the fundamental aspects of the adsorption process. These findings contribute to the development of advanced hydrogen storage and separation technologies, paving the way for efficient and sustainable energy applications.

Review of Molecular Dynamics Simulations of Phosphonium Ionic Liquid Lubricants

Phosphonium ionic liquids (ILs) have various uses, including as environmentally benign lubricants and lubricant additives. The properties and behavior of these ILs depend on their chemical composition, i.e., cation and anion combination, and the operating conditions. One approach to understanding the relationships between composition, conditions, and lubricant-relevant properties is classical molecular dynamics simulation. Although this research area is still emerging, it is growing rapidly, so a review of the topic is timely. Here, we review force field-based molecular dynamics simulations of phosphonium ILs, with emphasis on physical, chemical, and thermal properties relevant to lubricants. Properties reported in previous studies are density, viscosity, self-diffusivity, ionic conductivity, heat capacity, and thermal stability, as well as interactions with other compounds, including \(\mathrm {H_2O}\) and \(\mathrm {CO_2}\), and solid surfaces. The effects of anion and cation, as well as conditions such as temperature, on these properties are identified and analyzed in terms of anion-cation structure, orientation, and interactions. Finally, trends are summarized and opportunities for future research are identified.Graphical Abstract

Predicting CaO-(MgO)-Al2O3-SiO2 glass reactivity in alkaline environments from force field molecular dynamics simulations

In this investigation, force field-based molecular dynamics (MD) simulations have been employed to generate detailed structural representations for a range of amorphous quaternary CaO-MgO-Al2O3-SiO2 (CMAS) and ternary CaO-Al2O3-SiO2 (CAS) glasses. Comparison of the simulation results with select experimental X-ray and neutron total scattering and literature data reveals that the MD-generated structures have captured the key structural features of these CMAS and CAS glasses. Based on the MD-generated structural representations, we have developed two structural descriptors, specifically (i) average metal oxide dissociation energy (AMODE) and (ii) average self-diffusion coefficient (ASDC) of all the atoms at melting. Both structural descriptors are seen to more accurately predict the relative glass reactivity than the commonly used degree of depolymerization parameter, especially for the eight synthetic CAS glasses that span a wide compositional range. Hence these descriptors hold great promise for predicting CMAS and CAS glass reactivity in alkaline environments from compositional information.

Reactive Force Field-Based Molecular Dynamics Simulations on the Thermal Stability of Trimesic Acid on Graphene: Implications for the Design of Supramolecular Networks

Reactive Force Field-Based Molecular Dynamics Simulations on the Thermal Stability of Trimesic Acid on Graphene: Implications for the Design of Supramolecular Networks

Illuminating Invisible Grain Boundaries in Coalesced Single-Orientation WS2 Monolayer Films.

Engineering atomic-scale defects is crucial for realizing wafer-scale, single-crystalline transition metal dichalcogenide monolayers for electronic devices. However, connecting atomic-scale defects to larger morphologies poses a significant challenge. Using electron microscopy and ReaxFF reactive force field-based molecular dynamics simulations, we provide insights into WS2 crystal growth mechanisms, providing a direct link between synthetic conditions and microstructure. Dark-field TEM imaging of coalesced monolayer WS2 films illuminates defect arrays that atomic-resolution STEM imaging identifies as translational grain boundaries. Electron diffraction and high-resolution imaging reveal that the films have nearly a single orientation with imperfectly stitched domains that tilt out-of-plane when released from the substrate. Imaging and ReaxFF simulations uncover two types of translational mismatch, and we discuss their origin related to relatively fast growth rates. Statistical analysis of >1300 facets demonstrates that microstructural features are constructed from nanometer-scale building blocks, describing the system across sub-Ångstrom to multimicrometer length scales.

Steric and Electrostatic Effects on the Diffusion of CH4/CH3OH in Copper-Exchanged Zeolites: Insights from Enhanced Sampling Molecular Dynamics and Free Energy Calculations.

Copper-exchanged zeolites have demonstrated high selectivity in methane-to-methanol conversion carried out on copper-oxo centers. Nevertheless, the reaction can only occur if the methane molecules reach the active site while the methanol molecules must leave the material without high energetic cost for the migration. In this context, we have used force field-based molecular dynamics simulations with the potential of mean force method to estimate the energy barrier in cage to cage diffusion of methane and methanol molecules in the chabazite framework type zeolite. The results show considerably higher energy barrier for methanol diffusion. The steric effect of the active site and the electrostatic environment favors the CH3OH diffusion toward nonactive cages where it tends to accumulate due to the strong interactions with the zeolite. The same behavior is observed in the water molecules distribution, which emphasizes the control of the electrostatic potential over the polar molecules migration. For high concentration of polar molecules, the electrostatic effect is shielded and the driving force is reduced for CH3OH diffusion. The results show that if the electrostatic environment can be controlled, the product migration may be facilitated, which can improve the catalytic process.

Inclusion Complexation of Organic Micropollutants with β-Cyclodextrin.

Recently, β-cyclodextrin (βCD)-based polymers with enhanced adsorption kinetics and high removal capacity of organic micropollutants (OMPs) and uptake rates have been synthesized and tested experimentally. Although the exact physical–chemical mechanisms via which these polymers capture the various types of OMPs are not yet fully understood, it is suggested that the inclusion complex formation of OMPs with βCD is very important. In this study, the inclusion complex formation of OMPs with βCD in an aqueous solution is investigated by using the well-established attach–pull–release method in force field-based molecular dynamics simulations. A representative set of OMPs is selected based on the measured occurrences in surface and ground waters and the directives published by the European Union. To characterize the formation of the inclusion complex, the binding free energies, enthalpies, and entropies are computed and compared to experimental values. It is shown that computations using the q4md-CD/GAFF/Bind3P force field combination yield binding free energies that are in reasonable agreement with the experimental results for all OMPs studied. The binding enthalpies are decomposed into the main contributing interaction types. It is shown that, for all studied OMPs, the van der Waals interactions are favorable for the inclusion complexion and the hydrogen bond formation of the guest with the solvent and βCD plays a crucial role in the binding mechanism. Our findings show that MD simulations can adequately describe the inclusion complex formation of βCD with OMPs, which is the first step toward understanding the underlying mechanisms via which the βCD-based polymers capture OMPs.

Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids.

Cysteine is the only coded amino acid in biology that contains a thiol functional group. Deprotonated thiolate is essential for anchoring iron-sulfur ([Fe-S]) clusters, as prosthetic groups to the protein matrix. [Fe-S] metalloproteins and metalloenzymes are involved in biological electron transfer, radical chemistry, small molecule activation and signalling. These are key metabolic and regulatory processes that would likely have been present in the earliest organisms. In the context of emergence of life theories, the selection and evolution of the cysteine-specific R-CH2-SH side chain is a fascinating question to confront. We undertook a computational [4Fe-4S]-maquette modelling approach to evaluate how side chain length can influence [Fe-S] cluster binding and stability in short 7-mer and long 16-mer peptides, which contained either thioglycine, cysteine or homocysteine. Force field-based molecular dynamics simulations for [4Fe-4S] cluster nest formation were supplemented with density functional theory calculations of a ligand-exchange reaction between a preassembled cluster and the peptide. Secondary structure analysis revealed that peptides with cysteine are found with greater frequency nested to bind preformed [4Fe-4S] clusters. Additionally, the presence of the single methylene group in cysteine ligands mitigates the steric bulk, maintains the H-bonding and dipole network, and provides covalent Fe-S(thiolate) bonds that together create the optimal electronic and geometric structural conditions for [4Fe-4S] cluster binding compared to thioglycine or homocysteine ligands. Our theoretical work forms an experimentally testable hypothesis of the natural selection of cysteine through coordination chemistry.

Reaction Mechanisms and Interfacial Behaviors of Sodium Silicate Glass in an Aqueous Environment from Reactive Force Field-Based Molecular Dynamics Simulations

Corrosion of silicate glasses in aqueous environment is common and it impacts many physical and chemical properties of these materials that have wide ranges of industrial and technological applicat...

Topological Control of Water Reactivity on Glass Surfaces: Evidence of a Chemically Stable Intermediate Phase

Glass surfaces are of considerable interest due to their disproportionately large influence on the performance of glass articles in many applications. However, the behavior of glass surfaces has proven difficult to model and predict due to their complex structure and interactions with the environment. Here, the effects of glass network topology on the surface reactivity of glasses have been investigated using reactive and nonreactive force field-based molecular dynamics simulations as well as density functional theory. A topological constraint-based description for surface reactivity is developed, allowing for improved understanding of the physical and chemical origins of surface reactivity. Results show evidence for the existence of a chemically stable intermediate phase on the surface of the glass where the glass network is mechanically isostatic.

Atomistic Simulations of Al(100) and Al(111) Surface Oxidation: Chemical and Topological Aspects of the Oxide Structure

The chemical and topological aspects of short- and medium-range atomic ordering on oxidized Al(100) and Al(111) surfaces have been studied by employing reactive force field-based molecular dynamics (ReaxFF-MD) simulations as a function of O2 gas density at 300 K. We found two oxide film growth regimes, compatible with experimental and recent modeling data. Trend of changes in oxide film thickness with increasing oxygen gas density agrees with available literature data, while slightly thicker oxide film forms on the Al(100) substrate. Chemical descriptors of short- and medium-range correlation manifest difference in atom environment between two ultrathin oxide films as [3,4]Al and [2,3]O-coordinated species dominate. In turn, a highly liquid-like structure of ultrathin oxide film develops on the Al(100) surface compared to an amorphous nature of the Al(111) oxide film with slightly lower thickness. Three-dimensional analysis of oxide structures reveals a medium-range atomic order formed by the arrangement ...

Reactive Molecular Dynamics Simulations of Self-Assembly of Polytwistane and Its Application for Nanofibers

We investigated the self-assembly and mechanical properties of polytwistane (PT), particularly a seven-strand PT rope, using reactive force field-based molecular dynamics simulations at different temperatures. We show that upon self-assembly due to strong van der Waals interaction among PT units, PTs form a twisted structure (ropelike) with a twisting angle of ∼0.16 rad/nm at 300 K, which makes them mechanically stronger. The PT rope has high Young’s modulus (∼0.45 TPa) at 300 K. Interestingly, Young’s modulus increases with temperature for the seven-strand PT rope, whereas it decreases with temperature for a single-strand PT. This is because in the case of the seven-strand PT, the twisting angle also contributes to the elastic property of the PT rope and twisting depends on the temperature. We estimate a maximum load transfer of ∼1.1 and ∼3.3 nN to the central unit at 100 and 300 K, respectively. Hence, the amount of load transfer critically depends on the twisting in the rope. The fracture behavior of t...

Nanoporous silica gel structures and evolution from reactive force field-based molecular dynamics simulations

Nanoporous silica-rich gel formed on silicate glass surfaces during dissolution in aqueous environment is critical in elucidating the corrosion mechanisms and the long-term residual dissolution behaviors. Silica gel models were created using two types of methods with reactive force field-based molecular dynamics simulations. The results show that the remnant silica gels created from the ISG bulk structure have a more isolated and closed pore morphology and slightly higher glass network connectivity. This contrasts with the gel structures created by hydrogarnet defect formation that exhibit more connected pore morphologies. The remnant gel structures show lower water diffusivity which was explained by the nano-confinement effect of water molecules due to frequent interactions of water molecules with adjacent silica walls and the more isolated pore morphology in the remnant gel structures. These results reveal the complexity in terms of micro and atomic structures of these silica gels, and both structure features have impact on water transport in the gel layer hence the passivating effect that controls the long-term dissolution behavior of these glasses.

Superlubricity of epitaxial monolayer WS2 on graphene

We report the superlubric sliding of monolayer tungsten disulfide (WS2) on epitaxial graphene (EG) grown on silicon carbide (SiC). Single-crystalline WS2 flakes with lateral size of hundreds of nanometers are obtained via chemical vapor deposition (CVD) on EG. Microscopic and diffraction analyses indicate that the WS2/EG stack is predominantly aligned with zero azimuthal rotation. The present experiments show that, when perturbed by a scanning probe microscopy (SPM) tip, the WS2 flakes are prone to slide over the graphene surfaces at room temperature. Atomistic force field-based molecular dynamics simulations indicate that, through local physical deformation of the WS2 flake, the scanning tip releases enough energy to the flake to overcome the motion activation barrier and trigger an ultralow-friction rototranslational displacement, that is superlubric. Experimental observations show that, after sliding, the WS2 flakes come to rest with a rotation of nπ/3 with respect to graphene. Moreover, atomically resolved measurements show that the interface is atomically sharp and the WS2 lattice is strain-free. These results help to shed light on nanotribological phenomena in van der Waals (vdW) heterostacks, and suggest that the applicative potential of the WS2/graphene heterostructure can be extended by novel mechanical prospects.

Charge Environment and Hydrogen Bond Dynamics in Binary Ionic Liquid Mixtures: A Computational Study.

The extent of charge transfer between the cation and the anion in a room-temperature ionic liquid depends on the basicity of the anion. Ion charges determined in the condensed state via density functional theory calculations capture this effect rather well, and charges derived in such a manner have been employed in force field-based molecular dynamics simulations to quantitatively reproduce several physical properties of the liquids. However, the issue of transferability of cation charges in mixtures of ionic liquids, say with one type of cation and two different anion types needs to be addressed. Herein, we demonstrate that the cation charge in such a mixture varies linearly with anion composition, a result that ties in rather well with X-ray photoelectron spectroscopic experiments. The variation in cation charge with bulk anion composition is shown to be a result of changes in its coordination environment. Cations surrounded by a higher proportion of more basic anions possess lower charges than those surrounded by less basic anions. Time scales for the exchange of anion types for the occupation of hydrogen bonding sites around the cation have been determined and are seen to be constituted by three processes-breakage of existing hydrogen bond, diffusion to the hydrogen bonding site and displacement of the incumbent anion from its site in the cation coordination shell. These time scales explain the differences observed between infrared and NMR spectroscopic experiments in ionic liquid mixtures rather well.