Improvement of the ReaxFF Description for Functionalized Hydrocarbon/Water Weak Interactions in the Condensed Phase

Advancing plant cell wall modelling: Atomistic insights into cellulose, disordered cellulose, and hemicelluloses - A review

The complexity of plant cell walls on different hierarchical levels still impedes the detailed understanding of biosynthetic pathways, interferes with processing in industry and finally limits applicability of cellulose materials. While there exist many challenges to readily accessing these hierarchies at (sub-) angström resolution, the development of advanced computational methods has the potential to unravel important questions in this field. Here, we summarize the contributions of molecular dynamics simulations in advancing the understanding of the physico-chemical properties of natural fibres. We aim to present a comprehensive view of the advancements and insights gained from molecular dynamics simulations in the field of carbohydrate polymers research. The review holds immense value as a vital reference for researchers seeking to undertake atomistic simulations of plant cell wall constituents. Its significance extends beyond the realm of molecular modeling and chemistry, as it offers a pathway to develop a more profound comprehension of plant cell wall chemistry, interactions, and behavior. By delving into these fundamental aspects, the review provides invaluable insights into future perspectives for exploration. Researchers within the molecular modeling and carbohydrates community can greatly benefit from this resource, enabling them to make significant strides in unraveling the intricacies of plant cell wall dynamics.

Molecular Dynamics Simulations of Soft and Reactive Landing of Proteins Desorbed by Argon Cluster Bombardment

Reactive molecular dynamics (MD) simulations were conducted to investigate the soft and reactive landing of hyperthermal velocity proteins transferred to a vacuum using large argon clusters. Experimentally, the interaction of argon cluster ion beams (Ar1000-5000+) with a target biofilm was previously used in such a manner to transfer lysozymes onto a collector with the retention of their bioactivity, paving the way to a new solvent-free method for complex biosurface nanofabrication. However, the experiments did not give access to a microscopic view of the interactions needed for their full understanding, which can be provided by the MD model. Our reactive force field simulations clarify the landing mechanisms of the lysozymes and their fragments on collectors with different natures (gold- and hydrogen-terminated graphite). The results highlight the conditions of soft and reactive landing on rigid surfaces, the effects of the protein structure, energy, and incidence angle before landing, and the adhesion forces with the collector substrate. Many of the obtained results can be generalized to other soft and reactive landing approaches used for biomolecules such as electrospray ionization and matrix-assisted laser desorption ionization.

LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations

Generating simulation-ready molecular models for the LAMMPS molecular dynamics (MD) simulation software package is a difficult task and impedes the more widespread and efficient use of MD in materials design and development. Fixed-bond force fields generally require manual assignment of atom types, bonded interactions, charges, and simulation domain sizes. A new LAMMPS pre- and postprocessing toolkit (LUNAR) is presented that efficiently builds molecular systems for LAMMPS. LUNAR automatically assigns atom types, generates bonded interactions, assigns charges, and provides initial configuration methods to generate large molecular systems. LUNAR can also incorporate chemical reactivity into simulations by facilitating the use of the REACTER protocol. Additionally, LUNAR provides postprocessing for free volume calculations, cure characterization calculations, and property predictions from LAMMPS thermodynamic outputs. LUNAR has been validated via building and simulation of pure epoxy and cyanate ester polymer systems with a comparison of the corresponding predicted structures and properties to benchmark values, including experimental results from the literature. LUNAR provides the tools for the computationally driven development of next-generation composite materials in the Integrated Computational Materials Engineering (ICME) and Materials Genome Initiative (MGI) frameworks. LUNAR is written in Python with the usage of NumPy and can be used via a graphical user interface, a command line interface, or an integrated design environment. LUNAR is freely available via GitHub.

Predicted Fracture Tendency of Naturally Occurring Aluminum Surface Coatings under Tensile Loading

Naturally occurring coatings on aluminum metal, such as its oxide or hydroxide, serve to protect the material from corrosion. Understanding the conditions under which these coatings mechanically fail is therefore expected to be an important aspect of predictive models for aluminum component lifetimes. To this end, we develop and apply a molecular dynamics (MD) modeling framework for conducting tension tests that is capable of isolating factors governing the mechanical strength as a function of coating chemistry, defect morphology, and variables associated with the loading path. We consider two representative materials, including γ-Al2O3 and γ-Al(OH)3 (i.e., oxide and hydroxide), both of which form readily as aluminum surface coatings. Our results indicate that defects have a significant bearing on the strength of aluminum oxide, with grain boundaries serving to reduce the strain at failure from εzz = 0.300 to 0.219, relative to perfect single crystal. Our simulations also predict that porosity lowers the elastic stiffness and yield strength of the oxide. Relative to perfect crystal, we find porosity factors of 5%, 10% and 20% decrease the yield stress by 26%, 36% and 53%, respectively. MD predicts that perfect hydroxide and oxide single crystal have respective strains at failure of 0.08 and 0.31 under tensile uniaxial strain loading, and that the corresponding yield stresses are respectively 1.6 and 11.1 GPa. These data indicate that the hydroxide is substantially more susceptible to mechanical failure than the oxide. Our results, coupled with literature findings that indicate hot and humid conditions favor formation of hydroxide and defective oxide coatings, indicate the potential for a complicated dependence of aluminum corrosion susceptibility and stress corrosion cracking on aging history.

Effect of Hyperthermal Hybrid Gas Composition on the Interfacial Oxidation and Nitridation Mechanisms of Graphene Sheet

Graphene is one of the most promising thermal protection materials for high-speed aircraft due to its lightweight and excellent thermophysical properties. At high Mach numbers, the extremely high postshock temperature would dissociate the surrounding air into a mixture of atomic and molecular components in a highly thermochemical nonequilibrium state, which greatly affects the subsequent thermal chemical reactions of the graphene interface. Through establishing a reactive gas-solid interface model, the reactive molecular dynamics method is employed in this study to reveal the influences of the thermochemical nonequilibrium gas mixture on the thermal oxidation and nitridation mechanisms of graphene sheet. The results show that three distinctive stages can be recognized during bombardment of various nonequilibrium gas components toward the graphene sheet: (i) collision and surface adsorption stage, (ii) gas-solid heterogeneous reaction stage, and (iii) gas phase homogeneous reaction stage. The surface catalysis effect is found to be dominant during the first two stages, which can influence the following ablation behavior of graphene significantly at high-temperature conditions. Moreover, surface catalysis, oxidation, nitridation, and ablation mechanisms between nonequilibrium gas and graphene interface are revealed, which is of high relevance for future interfacial design and application of graphene as a thermal protection material.

Hierarchical and reconfigurable interfibrous interface of bioinspired Bouligand structure enabled by moderate orderliness

Introducing natural Bouligand structure into synthetics is expected to develop high-performance structural materials. Interfibrous interface is critical to load transfer, and mechanical functionality of bioinspired Bouligand structure yet receives little attention. Here, we propose one kind of hierarchical and reconfigurable interfibrous interface based on moderate orderliness to mechanically reinforce bioinspired Bouligand structure. The interface imparted by moderate alignment of adaptable networked nanofibers hierarchically includes nanofiber interlocking and hydrogen-bonding (HB) network bridging, being expected to facilitate load transfer and structural stability through dynamic adjustment in terms of nanofiber sliding and HB breaking-reforming. As one demonstration, the hierarchical and reconfigurable interfibrous interface is constructed based on moderate alignment of networked bacterial cellulose nanofibers. We show that the resultant bioinspired Bouligand structural material exhibits unusual strengthening and toughening mechanisms dominated by interface-microstructure multiscale coupling. The proposed interfibrous interface enabled by moderate orderliness would provide mechanical insight into the assembly of widely existing networked nanofiber building blocks toward high-performance macroscopic bioinspired structural assemblies.

Simulation data for engineering graphene quantum dot epoxy nanocomposites using molecular dynamics

Graphene quantum dots (GQDs) were reported to fill the role of nanofillers that enhance composite properties. Detailed investigation of this nanofiller in composites is largely unexplored. To understand the fundamental mechanisms in play, this study uses molecular dynamics simulations to reveal the effects of GQDs on epoxy properties. Mechanical simulations were performed on three varying GQD chemistries which included a pristine GQD and 2 edge aminated GQDs with different degrees of functionalization (5.2 % and 7.6 %). These GQDs were separately inserted in a polymer matrix across five individual replicates. The nanocomposite mechanical properties were computed using uniaxial strain simulations to display the effect of embedded GQDs.

Development and validation of a general-purpose ReaxFF reactive force field for earth material modeling

ReaxFF reactive force field bridges the gap between nonreactive molecular simulations and quantum mechanical calculations and has been widely applied during the past two decades. However, its application to earth materials, especially those under high T-P conditions relevant to Earth's interior, is still limited due to the lack of available parameters. Here, we present the development and validation of a ReaxFF force field containing several of the most common elements in Earth's crust, i.e., Si/Al/O/H/Na/K. The force field was trained against a large data set obtained from density functional theory (DFT) calculations, including charges, bond/angle distortion curves, equation of states, ion migration energy profiles, and condensation reaction energies. Different coordination environments were considered in the training set. The fitting results showed that the current force field can well reproduce the DFT data (the Pearson correlation coefficient, Rp, is 0.95). We validated the force field on mineral-water interfaces, hydrous melts/supercritical geofluids, and bulk crystals. It was found that the current force field performed excellently in predicting the structural, thermodynamic, and transport properties of various systems (Rp = 0.95). Moreover, possible applications and future development have been discussed. The results obtained in this study suggest that the current force field holds good promise to model a wide range of processes and thus open opportunities to advance the application of ReaxFF in earth material modeling.

Mechanical properties and physicochemical characteristics of cotton fibers during combing process

This study employs a combination of experiments and molecular dynamics to analyze the mechanical properties and surface damage characteristics of cotton fibers during the combing process. Additionally, it investigates the alterations in physical and chemical properties at the atomic scale resulting from mechanical damage. Raw cotton (RC) is combed to 1st combed cotton (1st CC), 2nd combed cotton (2nd CC) and 3rd combed cotton (3rd CC). It was found that the mechanical properties and crystallinity showed an increasing and then decreasing trend with the process of combing, and the degree of surface tearing increased, and the binding energy of C and O shifted to a lower position. The breaking strength of cotton fibers first increased by 7.4 % and then decreased by 11 % and 7.7 % respectively, and the crystallinity was CrI (RC) = 70.8 %, CrI (1st CC) = 75.3 %, CrI (2nd CC) = 72.7 %, and CrI (3rd CC) = 71.8 % respectively. The C-O bond and the C-C bond at the amorphous regions are broken after combing lead to the cellulose chain to break, resulting in a decrease in the breaking strength of the fibers. The C-O bond as well as the C-O-C bond angles changes significantly during stretching, and the increase in ordering of the amorphous regions causes an increase in crystallinity.

Artificial Neural Networks for Predicting Mechanical Properties of Crystalline Polyamide12 via Molecular Dynamics Simulations

Predicting material properties of 3D printed polymer products is a challenge in additive manufacturing due to the highly localized and complex manufacturing process. The microstructure of such products is fundamentally different from the ones obtained by using conventional manufacturing methods, which makes the task even more difficult. As the first step of a systematic multiscale approach, in this work, we have developed an artificial neural network (ANN) to predict the mechanical properties of the crystalline form of Polyamide12 (PA12) based on data collected from molecular dynamics (MD) simulations. Using the machine learning approach, we are able to predict the stress-strain relations of PA12 once the macroscale deformation gradient is provided as an input to the ANN. We have shown that this is an efficient and accurate approach, which can provide a three-dimensional molecular-level anisotropic stress-strain relation of PA12 for any macroscale mechanics model, such as finite element modeling at arbitrary quadrature points. This work lays the foundation for a multiscale finite element method for simulating semicrystalline polymers, which will be published as a separate study.

Evolution of Glassy Carbon Derived from Pyrolysis of Furan Resin

Glassy carbon (GC) material derived from pyrolyzed furan resin was modeled by using reactive molecular dynamics (MD) simulations. The MD polymerization simulation protocols to cure the furan resin precursor material are validated via comparison of the predicted density and Young's modulus with experimental values. The MD pyrolysis simulations protocols to pyrolyze the furan resin precursor is validated by comparison of calculated density, Young's modulus, carbon content, sp2 carbon content, the in-plane crystallite size, out-of-plane crystallite stacking height, and interplanar crystallite spacing with experimental results from the literature for furan resin derived GC. The modeling methodology established in this work can provide a powerful tool for the modeling-driven design of next-generation carbon-carbon composite precursor chemistries for thermal protection systems and other high-temperature applications.

Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision

The bombardment of a protein multilayer target by an energetic argon cluster ion beam enables protein transfer onto a collector in the vacuum while preserving their bioactivity (iBEAM method). In parallel to this new soft-landing variant, protein transfer in the gas phase is a prerequisite for their characterization by mass spectrometry. The successful transfer of bioactive lysozymes (14 kDa) by cluster-induced soft landing and its mechanistic explanation by molecular dynamics (MD) simulations have sparked an important inquiry: Can heavier biomolecules be desorbed while maintaining their tridimensional structure and hence their bioactivity? To address this question, we employed MD simulations using a reactive force field (ReaxFF). Specifically, the Ar cluster-induced desorption of glucose oxidase from either a gold substrate or a lysozyme underlayer was modeled using the LAMMPS code. First, the force field parameters were trained by computing the dissociation energetics of a series of organic molecules with ReaxFF and DFT, in order to realistically describe N-S and O-S interactions in the bombarded glucose oxidase molecule. Second, bombardment simulations investigated the effects of cluster size (ranging from 1000 to 10000 Ar atoms) and kinetic energy (1.5 and 3.0 eV/atom) on the structural features and energetics of the desorbing glucose oxidase. Our results show that large argon clusters (≥7000) are needed to desorb glucose oxidase from a gold surface, yet protein fragmentation and/or pronounced denaturation occur. However, the transfer of structurally preserved glucose oxidase in the gas phase is predicted by the simulations when an organic layer is used as a substrate.

Accelerated Design of Ultra-High-Performance Aramid Copolymers via a High-Throughput Screening Approach

Developing advanced materials, such as functional polymers, poses a significant challenge as a result of the vastness of the material space that needs to be explored, which could potentially be infinite in principle. We propose a data-driven high-throughput screening approach coupled with molecular dynamics (MD) simulations to address this issue in the design of high-performance co-polymerized aramid fibers. We aimed to identify diamine monomers that could replace 3,4'-oxydianiline in Technora from a large-scale set (1 920 304) of possible monomers that were prepared from the PubChem database. We initially screened these monomers using a cheminformatics-based approach, considering four criteria: complexity, neutrality, linearity, and gyration radius of the molecule. Then, we performed subsequent screening based on MD simulations to estimate interchain interaction energies under both stretched and melted conditions and tensile strength simulations. Our screening approach successfully identified 31 promising and novel diamine monomers for aramid copolymers. This demonstrates the potential and effectiveness of our approach as a promising protocol for exploring targeted chemical spaces in designing novel monomers for high-performance aramid fibers and possibly other advanced polymers.

The Dynamic Nature of Graphene Active Sites in the H2O Gasification process: A ReaxFF and DFT Study

CONTEXT

A steam-rich environment is a more promising application scenario for future coal-fired processes, while active sites are the key factor that determines the reactivity of carbonaceous fuels. The steam gasification process of carbon surfaces with different numbers of active sites (0, 12, 24, 36) was simulated using reactive molecular dynamics in the present study. The temperature for the decomposition of H₂O and the gasification of carbon is determined using temperature-increasing simulation. The decomposition of H₂O was influenced by two driving forces, thermodynamics and active sites on the carbon surface, which dominated the different reaction stages, leading to the observed segmentation phenomenon of the H₂ production rate. The existence and number of initial active sites have a positive correlation with both two stages of the reaction, greatly reducing the activation energy. Residual OH groups play an important role in the gasification of carbon surfaces. The supply of OH groups through the cleavage of OH bonds in H₂O is the rate-limiting step in the carbon gasification reaction. The adsorption preference at carbon defect sites was calculated using density functional theory. Two stable configurations (ether & semiquinone groups) can be formed with O atoms adsorbed on the carbon surface according to the number of active sites. This study will provide further insights into the tuning of active sites for advanced carbonaceous fuels or materials.

METHODS

The large-scale atomic/molecule massively parallel simulator (LAMMPS) code combined with the reaction force-field method was used to carry out the ReaxFF molecular dynamics simulation, where the ReaxFF potentials were taken from Castro-Marcano, Weismiller and William. The initial configuration was built using Packmol, and the visualization of the calculation results was realized through Visual Molecular Dynamics (VMD). The timestep was set to 0.1 fs to detect the oxidation process with high precision. PWscf code in QUANTUM ESPRESSO (QE) package, was used to evaluate the relative stability of different possible intermediate configurations and the thermodynamic stability of gasification reactions. The projector augmented wave (PAW) and the generalized gradient approximation of Perdew-Burke-Ernzerhof (PBE-GGA) were adopted. Kinetic energy cutoffs of 50 Ry and 600 Ry, and a uniform mesh of 4 × 4 × 1 k-points were used.

Comparison of Force Fields for the Prediction of Thermophysical Properties of Long Linear and Branched Alkanes

The prediction of thermophysical properties at extreme conditions is an important application of molecular simulations. The quality of these predictions primarily depends on the quality of the employed force field. In this work, a systematic comparison of classical transferable force fields for the prediction of different thermophysical properties of alkanes at extreme conditions, as they are encountered in tribological applications, was carried out using molecular dynamics simulations. Nine transferable force fields from three different classes were considered (all-atom, united-atom, and coarse-grained force fields). Three linear alkanes (n-decane, n-icosane, and n-triacontane) and two branched alkanes (1-decene trimer and squalane) were studied. Simulations were carried out in a pressure range between 0.1 and 400 MPa at 373.15 K. For each state point, density, viscosity, and self-diffusion coefficient were sampled, and the results were compared to experimental data. The Potoff force field yielded the best results.

Bidirectional Water-Stream Behavior on a Multifunctional Membrane for Simultaneous Energy Generation and Water Purification

Hydroelectric nanogenerators have been previously proposed to recycle various water resources and polluted water. However, as conventional hydroelectric nanogenerators only utilize water resources, they cannot provide a fundamental solution for water recycling. In this study, a water purification membrane is proposed that can simultaneously generate electricity during the purification process (electricity generation and purification membrane (EPM)) for water recycling. As polluted water passes through the EPM, the water is purified in the perpendicular direction, while electricity is simultaneously produced in the horizontal direction by the movement of ions. Notably, the EPM exhibits high energy generation performance (maximum power 16.44 µW and energy 15.16 mJ) by the streaming effect of water-streaming carbon nanotubes (CNTs). Moreover, by using a poly(acrylic acid)/carboxymethyl cellulose (PAA/CMC) binder to EPM, the energy-generation performance and long-term stability are substantially improved and outstanding mechanical stability is provided, regardless of the acidity of the water source (pH 1-10). More importantly, the EPM exhibits the water purification characteristics of >90% rejection of sub-10 nm pollutants and potentiality of ångstrom level cation rejection, with simultaneous and continuous energy generation. Overall, this study proposes an efficient EPM model, which can be potentially used as a next-generation renewable energy generation approach, thus laying the foundation for effective utilization of polluted water resources.

ReaxFF-based nonadiabatic dynamics method for azobenzene derivatives

ReaxFF reactive force fields have been parameterized for the ground and first excited states of azobenzene and its derivatives. In addition, an extended set of ab initio reference data ensures wide applicability, including to azosystems in complex environments. Based on the optimized force fields, nonadiabatic surface hopping simulations produce photoisomerization quantum yields and decay times of azobenzene, both in the gas phase and in n-hexane solution, in reasonable agreement with higher level theory and experiment. The transferability to other azo-compounds is illustrated for different arylazopyrazoles as well as ethylene-bridged azobenzene. Moreover, it has been shown that the model can be easily extended to adsorbates on metal surfaces. The simulation of the ring-opening of cyclobutene triggered by the photoisomerization of azobenzene in a macrocycle highlights the advantages of a reactive force field model.

Parallel-Self-Assembling Stack, Center-Capture Effect, and Reactivity-Enhancing Effect of N-Layer (N = 1, 2, 3) Cyclo[18]carbon

Cyclo[18]carbon (C₁₈) is an captivating allotrope of carbon synthesized recently, which has drawn the attention among scientists. There are still few studies on the dynamic behaviors of C₁₈. To gain knowledge in this area, we systematically explored the stacking behaviors and the oxidation kinetics of C₁₈, as well the electronic transport behaviors of C₁₈ oxides, by density functional theory and nonequilibrium Green's function calculations combined with reactive force field molecular dynamics simulations. The parallel-self-assembling behaviors were observed in the stack of two- or three-layer C₁₈. During the oxidation process of C₁₈, we found an evident center-capture effect in which the hollow rings would preferentially attract an O₂ molecule into their centers. Moreover, the adsorption of O₂ on the O₂-doped rings was dramatically enhanced by the O₂ at the center of the ring, showing the reactivity-enhancing effect. The excellent electron transport property of central-O₂-doped C₁₈ among 13 types of C₁₈ oxides demonstrates the potential of C₁₈ oxides as promising molecular devices for various applications. This study reveals the dynamic behaviors of C₁₈ and provides theoretical guidance for use of C₁₈ and C₁₈ oxides in molecular devices.

Aqueous Proton Transportation in Graphene-Based Nanochannels

Graphene oxide (GO) has been unveiled to exhibit high proton conductivity in a humidified or aqueous environment, making it a promising candidate to construct proton conduction nanochannels. In this work, we systematically investigate how the confinement effect and surface chemistry influence the proton transportation behavior in graphene-based nanochannels via extensive ReaxFF MD simulations. Graphene (GE), graphane (GA), and hydroxygraphane (HG) sheets were employed to mimic the graphitic and functionalized region of GO and construct nanochannels with different interlayer distances. We find that confined water molecules are stratified and their orientation is influenced by the surface chemistry, thus impacting the distribution of protons. Surface chemistry makes the compression of the hydrogen-bond network induced by the confinement effect more variable. The hydrogen-bond network between GE slabs is crushed by extreme confinement and ultrafast proton transportation behavior mainly achieved via vehicle mechanism. Meanwhile, the hydrogen-bond network and solvation structure can be kept more complete with the existence of functional groups. The hydrogen bonds formed with surface functional groups impede the transportation of water molecules but allow more Grotthuss hopping of protons to different extents. Our work clarified the proton transportation mechanism in graphene-based nanochannels with different interlayer distances and surface chemistry and can guide the future design of proton conduction devices such as proton exchange membranes.

Cellulose Nanocrystals: Tensile Strength and Failure Mechanisms Revealed Using Reactive Molecular Dynamics

Cellulose nanocrystals (CNCs) offer excellent mechanical properties. However, measuring the strength by performing reliable experiments at the nanoscale is challenging. In this paper, we model Iβ crystalline cellulose using reactive molecular dynamics simulations. Taking the fibril twist into account, structural changes and hydrogen-bonding characteristics of CNCs during the tensile test are inspected and the failure mechanism of CNCs is analyzed down to the scale of individual bonds. The C4-O4 glycosidic bond is found to be responsible for the failure of CNCs. Finally, the effect of strain rate on ultimate properties is analyzed and a nonlinear model is used to predict the ultimate strength of 9.2 GPa and ultimate strain of 8.5% at a 1 s^-1 strain rate. This study sheds light on the applications of cellulose in nanocomposites and further modeling of cellulose nanofibres.

Ab initio molecular dynamics study on the disordered Li-Ga-Sn system

The eutectic Ga_91.6Sn_8.4 liquid metal could serve as the anode in Li-ion batteries to avoid dendrite growth issue and volume expansion, and maintain a good cycle life. However, the microstructure and the basic physical properties of the lithiated Ga_91.6Sn_8.4 are ignored in experiments and still unclear. In this work, we assume that a disordered structure is formed in the initial stage of lithiation of Ga_91.6Sn_8.4, and the structure, equilibrium density, thermal expansion coefficient, mixing enthalpy, self-diffusion coefficient and viscosity of the disordered Li-Ga-Sn system are investigated systematically by ab initio molecular dynamics. The radial distribution function, structure factor and bond angle distribution function are calculated to obtain local structure information. Our calculations show that the lithiation of Ga_91.6Sn_8.4 is exothermic, and for most cases, the diffusion coefficients for Li, Ga and Sn decrease with increasing Li content. Based on structural information and diffusion coefficients, we reveal that the lithiation of Ga_91.6Sn_8.4 will make the liquid Ga_91.6Sn_8.4 alloy form a solid-like structure. With the increase of Li content, it is more likely to form a solid-like structure. Furthermore, our simulations reveal that the chemical interaction of Li-Sn and Li-Ga is stronger than that of Ga-Sn, and Li is prone to combine with Sn firstly in the lithiation process of Ga_91.6Sn_8.4.

Behavior of Linear and Nonlinear Dimensionality Reduction for Collective Variable Identification of Small Molecule Solution-Phase Reactions

Identifying collective variables (CVs) for chemical reactions is essential to reduce the 3N-dimensional energy landscape into lower dimensional basins and barriers of interest. However, in condensed phase processes, the nonmeaningful motions of bulk solvent often overpower the ability of dimensionality reduction methods to identify correlated motions that underpin collective variables. Yet solvent can play important indirect or direct roles in reactivity, and much can be lost through treatments that remove or dampen solvent motion. This has been amply demonstrated within principal component analysis (PCA), although less is known about the behavior of nonlinear dimensionality reduction methods, e.g., uniform manifold approximation and projection (UMAP), that have become recently utilized. The latter presents an interesting alternative to linear methods though often at the expense of interpretability. This work presents distance-attenuated projection methods of atomic coordinates that facilitate the application of both PCA and UMAP to identify collective variables in the presence of explicit solvent and further the specific identity of solvent molecules that participate in chemical reactions. The performance of both methods is examined in detail for two reactions where the explicit solvent plays very different roles within the collective variables. When applied to raw molecular dynamics data in solution, both PCA and UMAP representations are dominated by bulk solvent motions. On the other hand, when applied to data preprocessed by our attenuated projection methods, both PCA and UMAP identify the appropriate collective variables (though varying sensitivity is observed due to the presence of explicit solvent that results from the projection method). Importantly, this approach allows identification of specific solvent molecules that are relevant to the CVs and their importance.

M SB, George JJ, Rasulev B, Raghavan P. Experimental and Simulation Studies on Nonwoven Polypropylene-Nitrile Rubber Blend: Recycling of Medical Face Masks to an Engineering Product

The battle against the COVID-19 pandemic counters the waste management system, as billions of single-use face masks are used per day all over the world. Proper disposal of used face masks without jeopardizing the health and the environment is a challenge. Herein, a novel method for recycling of medical face masks has been studied. This method incorporates the nonwoven polypropylene (PP) fiber, which is taken off from the mask after disinfecting it, with acrylonitrile butadiene rubber (NBR) using maleic anhydride as the compatibilizer, which results in a PP-NBR blend with a high percentage economy. The PP-NBR blends show enhanced thermomechanical properties among which, 70 wt % PP content shows superior properties compared to other composites with 40, 50, and 60 wt % of PP. The fully Atomistic simulation of PP-NBR blend with compatibilizer shows an improved tensile and barrier properties, which is in good agreement with the experimental studies. The molecular dynamics simulation confirms that the compatibility between non-polar PP and polar NBR phases are vitally important for increasing the interfacial adhesion and impeding the phase separation.

Development of a Charge-Implicit ReaxFF for C/H/O Systems

Modeling chemical reactions in condensed phases is difficult. Interaction potentials (or force fields) like ReaxFF can perform this modeling with a high overall accuracy, but the disadvantage of ReaxFF is a low simulation speed arising from costly algorithms, in particular charge equilibration. Therefore, we reparametrized ReaxFF to incorporate Coulomb forces into other terms of the force field. Because of this change, our charge-implicit ReaxFF-CHO is >2 times faster than the original parametrization. Despite the lack of explicit electrostatic interactions, our potential can correctly model the reactions and densities of systems containing carbon, hydrogen, and oxygen atoms. We have used the new potential to simulate bombardment of trehalose by water clusters. It has been observed experimentally that these water projectiles can increase the sensitivity of secondary ion mass spectrometry by more than an order of magnitude, but no explanation for this phenomenon was given. Our simulations show that the increase in the intensity of the recorded signal coincides with the emission of trehalose-water complexes.

Investigating the Accuracy of Water Models through the Van Hove Correlation Function

We present molecular-simulation-based calculations of the Van Hove correlation function (VHF) of water using multiple modeling approaches: classical molecular dynamics with simple three-site nonpolarizable models, with a polarizable model, and with a reactive force field; density functional tight-binding molecular dynamics; and ab initio molecular dynamics. Due to the many orders of magnitude difference in the computational cost of these approaches, we investigate how small and short the simulations can be while still yielding sufficiently accurate and interpretable results for the VHF. We investigate the accuracy of the different models by comparing them to recently published inelastic X-ray scattering measurements of the VHF. We find that all of the models exhibit qualitative agreement with the experiments, and in some models and for some properties, the agreement is quantitative. This work lays the foundation for future simulation approaches to calculating the VHF for aqueous solutions in bulk and under nanoconfinement.

Thermophysical properties of water using reactive force fields

The widescale importance and rich phenomenology of water continue to motivate the development of computational models. ReaxFF force fields incorporate many characteristics desirable for modeling aqueous systems: molecular flexibility, polarization, and chemical reactivity (bond formation and breaking). However, their ability to model the general properties of water has not been evaluated in detail. We present comprehensive benchmarks of the thermophysical properties of water for two ReaxFF models, the water-2017 and CHON-2017_weak force fields. These include structural, electrostatic, vibrational, thermodynamic, coexistence, and transport properties at ambient conditions (300 K and 0.997 g cm^-3) and along the standard pressure (1 bar) isobar. Overall, CHON-2017_weak predicts more accurate thermophysical properties than the water-2017 force field. Based on our results, we recommend potential avenues for improvement: the dipole moment to quadrupole moment ratio, the self-diffusion coefficient, especially for water-2017, and the gas phase vibrational frequencies with the aim to improve the vibrational properties of liquid water.

Influence of stacking on the aqueous proton penetration behaviour across two-dimensional graphtetrayne

Two-dimensional (2D) graphtetrayne (G4) with intrinsic pattern triangular nanopores has been predicted to be an excellent candidate for next-generation proton exchange membranes due to its superior proton conductivity and selectivity. However, it is technically challenging to prepare a large area single-layer intact 2D material. A multi-layer stacked 2D material is a much more suitable choice, and the stacking can effectively shield the undesired defects and tears. In this work, we investigate the aqueous proton penetration behavior across multilayer-stacked two-dimensional G4 using extensive ReaxFF molecular dynamics simulations. We found that the G4 layers prefer a slightly misplaced stacking pattern which would cause only a slight reduction in the pore size. Detailed analyses indicate that the "water wires" across G4 remain continuous and can provide a low-barrier path for proton penetration until the number of stacking layers increases to three. In triple-layer G4, the "water wires" no longer exist and the aqueous phase will be separated by a wide vacuum area, thus significantly impeding the proton penetration behavior. Based on these results, we suggest that when serving as a proton exchange membrane, the number of stacking G4 layers should be fewer than three to achieve satisfactory conductivity. Our work provides guidance for the fabrication of next-generation proton exchange membranes based on nanoporous 2D materials.

Computational Assessment of the Three-Dimensional Configuration of Dissolved Organic Matter Chromophores and Influence on Absorption Spectra

The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Molecular dynamics simulations of DOM model compounds carefully selected based on ultrahigh-resolution mass spectrometry data revealed that, while DOM does indeed form molecular aggregates, the large majority of molecules (especially, O-atom bearing molecules) are solvent accessible. Additionally, these computations revealed that molecular aggregates are weak and dissociate when placed in organic solvents (tetrahydrofuran, methyl tert-butyl ether). Time-dependent density functional theory calculations demonstrated long-wavelength absorbance for both model DOM chromophores and their molecular aggregates. This study has important implications for determining the origin of DOM optical properties and for enhancing our collective understanding of DOM three-dimensional structures.

ReaxFF/AMBER-A Framework for Hybrid Reactive/Nonreactive Force Field Molecular Dynamics Simulations

Combined quantum mechanical/molecular mechanical (QM/MM) models using semiempirical and ab initio methods have been extensively reported on over the past few decades. These methods have been shown to be capable of providing unique insights into a range of problems, but they are still limited to relatively short time scales, especially QM/MM models using ab initio methods. An intermediate approach between a QM based model and classical mechanics could help fill this time-scale gap and facilitate the study of a range of interesting problems. Reactive force fields represent the intermediate approach explored in this paper. A widely used reactive model is ReaxFF, which has largely been applied to materials science problems and is generally used as a stand-alone (i.e., the full system is modeled using ReaxFF). We report a hybrid ReaxFF/AMBER molecular dynamics (MD) tool, which introduces ReaxFF capabilities to capture bond breaking and formation within the AMBER MD software package. This tool enables us to study local reactive events in large systems at a fraction of the computational costs of QM/MM models. We describe the implementation of ReaxFF/AMBER, validate this implementation using a benzene molecule solvated in water, and compare its performance against a range of similar approaches. To illustrate the predictive capabilities of ReaxFF/AMBER, we carried out a Claisen rearrangement study in aqueous solution. In a first for ReaxFF, we were able to use AMBER's potential of mean force (PMF) capabilities to perform a PMF study on this organic reaction. The ability to capture local reaction events in large systems using combined ReaxFF/AMBER opens up a range of problems that can be tackled using this model to address both chemical and biological processes.

A Reactive Force Field with Coarse-Grained Electrons for Liquid Water

Nonreactive force fields are defined by perturbations of electron density that are relatively small, whereas chemical reactivity involves wholesale electronic rearrangements that make and break bonds. Thus, reactive force fields are incredibly difficult to develop compared to nonreactive force fields, yet at the same time, they fill a critical need when ab initio molecular dynamics methods are not affordable. We introduce a new reactive force field model for water that combines modified nonbonded terms of the ReaxFF model and its embedding in the electrostatic interactions described by our recently introduced coarse-grained electron model (C-GeM). The ReaxFF/C-GeM force field is characterized for many energetic and dissociative water properties for water clusters, structure, and dynamical properties under ambient conditions in the condensed phase, as well as the temperature dependence of density and water diffusion, with very good agreement with experiment. The ReaxFF/C-GeM force field should be more transferable and more broadly applicable to a range of reactive systems involving both proton and electron transfer in the condensed phase.

Anisotropic hydrogen bond structures and orientation dependence of shock sensitivity in crystalline 1,3,5-tri-amino-2,4,6-tri-nitrobenzene (TATB)

The orientation dependence of shock sensitivity in high explosive crystals was explored in this study. As a widely used wood explosive, 1,3,5-tri-amino-2,4,6-tri-nitrobenzene (TATB) is insensitive to thermal ignition and mechanical impact. Its typical anisotropic crystal structure suggests anisotropic shock sensitivity. Shockwaves were applied to an incised TATB crystal along three orthogonal directions using the multiscale shock technique (MSST) combined with the ReaxFF method to study the origin of anisotropic shock sensitivity. The physical and chemical responses of the TATB crystal during shock were investigated. The results show that the temperature, stress, volume compressibility, and decomposition rate of TATB are strongly dependent on the shockwave direction. In other words, the sensitivity of TATB to mechanical shock is strongly dependent on the crystal orientation. TATB is relatively sensitive along the directions parallel to the (001) crystal plane (X and Y directions) and is highly insensitive along the [001] direction (Z direction). We calculated the energy of intermolecular hydrogen bonds and the elastic constants of the TATB crystal using ab initio simulations, which also show anisotropy. We found that the unique structure of intermolecular hydrogen bonds and the difference in temperature rise induced by orientation-related compressibility are primarily responsible for the anisotropic shock wave sensitivity.

Oxidation of graphene with variable defects: alternately symmetrical escape and self-restructuring of carbon rings

Variable defects such as vacancies and grain boundaries are unavoidable in the synthesis of graphene, but play a central role in the activation of oxidation. Here, we apply reactive molecular dynamics simulations to reveal the underpinning mechanisms of oxidation in graphene with or without defects at the atomic scale. There exist four oxidation modes generating CO2 or CO in different stages, beginning from a single-atom vacancy, and proceeding until the ordered structure broken down into carbon oxide chains. The oxidation process of the graphene sheets experiences four typical stages, in which alternately symmetrical escape phenomenon is observed. Importantly, disordered rings can self-restructure during the oxidation of grain boundaries. Of all defects, the oxidation of vacancy has the lowest energy barrier and is therefore the easiest point of nucleation. This study demonstrates the crucial role of defects in determining the oxidation kinetics, and provides theoretical guidance for the oxidation prevention of graphene and the production of functionalized graphene.

Anomalous proton conduction behavior across a nanoporous two-dimensional conjugated aromatic polymer membrane

We investigate aqueous proton penetration behavior across a newly synthesized nanoporous two-dimensional conjugated aromatic polymer (2D-CAP) membrane using extensive ReaxFF reactive molecular dynamics simulations. We found that the proton penetration energy barrier across 2D-CAP is twice as high as that of graphtetrayne, even though 2D-CAP exhibits a larger pore size. Detailed analysis indicates that the anomalous high proton conduction energy barrier of 2D-CAP originates from its unique atomic nanopore structure. The hydrogen atoms at the periphery of the 2D-CAP nanopores can form a stable local hydrogen bond network with water molecules inside or surrounding the nanopores. The mobility of water molecules involved in this local hydrogen bond network will be significantly lowered, and the proton transportation process across the nanopores will thus be impeded. Our results show that the proton penetration behavior across nanoporous 2D materials is influenced not only by the pore size, but also by the decorated atoms or functional groups at the pore edges. Hydrogen atoms at the periphery of nanopores with certain geometry can form a stable local hydrogen bond network with neighboring water molecules, further hampering the proton conductivity.

Mechanical size effects of amorphous polymer-derived ceramics at the nanoscale: experiments and ReaxFF simulations

Here we report an unprecedented mechanical size effect at the nanoscale in polymer-derived ceramic (PDC) nanofibers. Silicon oxycarbide (SiOC) PDCs were fabricated as micro- and nanofibers without the aid of fillers. By decreasing the size of SiOC ceramic fibers from 1.1 μm to 630 nm (reduction of 74%), the strength of nanofibers nearly tripled, going from ∼1 GPa to ∼3.3 GPa. This increase in strength exceeds the predictions of the Griffith theorem, which relies on the length-scale dependence of energy release rate during crack propagation, suggesting a reduction in flaw size more than proportional to sample size. Given the crosslinked and amorphous nature of SiOC PDCs, flaws are likely microcracks and voids, which form during polymer degassing as it is pyrolyzed to PDC nanofibers. A reduction in sample size may favor degassing via diffusion, preceding bubble and void formation. We developed a new reactive force field (ReaxFF) with parameters for Si/O/C/H/N to study the mechanics of PDCs in extreme cases where no void is present. The models and experiments compare favorably in terms of the elastic modulus. The simulations suggest a strength of ∼8.5 GPa for a "flawless" structure, which is in line with extrapolated experimental results, with C-C breakage as the root cause of failure. This work clearly shows the benefits of utilizing nanoscale components as building blocks of superstrong PDC structures.

Origins of complex solvent effects on chemical reactivity and computational tools to investigate them: a review

Origins of solvent-induced enhancement in catalytic reactivity and product selectivity are discussed with computational methods to study them.

Ionized water confined in graphene nanochannels

When confined between graphene layers, water in the presence of additional hydronium and hydroxide ions exhibits distinct properties such as ion layering structure determined by the channel size, disruption of the ion solvation shell, and slower ion recombination rate as compared to bulk water.

Multiscale Modeling of Structure, Transport and Reactivity in Alkaline Fuel Cell Membranes: Combined Coarse-Grained, Atomistic and Reactive Molecular Dynamics Simulations

In this study, molecular dynamics (MD) simulations of hydrated anion-exchange membranes (AEMs), comprised of poly(p-phenylene oxide) (PPO) polymers functionalized with quaternary ammonium cationic groups, were conducted using multiscale coupling between three different models: a high-resolution coarse-grained (CG) model; Atomistic Polarizable Potential for Liquids, Electrolytes and Polymers (APPLE&P); and ReaxFF. The advantages and disadvantages of each model are summarized and compared. The proposed multiscale coupling utilizes the strength of each model and allows sampling of a broad spectrum of properties, which is not possible to sample using any of the single modeling techniques. Within the proposed combined approach, the equilibrium morphology of hydrated AEM was prepared using the CG model. Then, the morphology was mapped to the APPLE&P model from equilibrated CG configuration of the AEM. Simulations using atomistic non-reactive force field allowed sampling of local hydration structure of ionic groups, vehicular transport mechanism of anion and water, and structure equilibration of water channels in the membrane. Subsequently, atomistic AEM configuration was mapped to ReaxFF reactive model to investigate the Grotthuss mechanism in the hydroxide transport, as well as the AEM chemical stability and degradation mechanisms. The proposed multiscale and multiphysics modeling approach provides valuable input for the materials-by-design of novel polymeric structures for AEMs.

Isotope Effects in Water: Differences of Structure, Dynamics, Spectrum, and Proton Transport between Heavy and Light Water from ReaxFF Reactive Force Field Simulations

Investigating properties of both heavy and light water at the atomistic level is essential to understanding chemical and biological processes in aqueous solution. However, appropriately describing their difference on the nanoscale is still challenging. Employing ReaxFF reactive molecular dynamics simulations, we systematically study the structure, dynamics, and spectra of heavy and light water. With the water force field potential we developed, the different features between heavy and light water can be simulated appropriately by the classical treatment on large size and time scale. Here, we also report the structural difference between D₃O⁺ and H₃O⁺ in bulk heavy/light water. In addition, the diffusion constants of heavy and light water are successfully reproduced, and the Grotthuss hopping mechanism of proton transport in liquid water is properly described as well. It allows us to study a complex system in heavy/light aqueous environments, such as proton transport, chemical reaction, and tracing the reaction mechanism with an isotope substitute.