Classical Reactive Molecular Dynamics Research Articles

Irida-graphene phonon thermal transport via non-equilibrium molecular dynamics simulations.

Recently, a new 2D carbon allotrope called Irida-Graphene (Irida-G) was proposed, and its reliable stability has been previously predicted. Irida-G is a flat sheet topologically arranged into 3-6-8 carbon rings exhibiting metallic and non-magnetic properties. In this study, we investigated the thermal transport properties of Irida-G using classical reactive molecular dynamics simulations. The findings indicate that Irida-G has an intrinsic thermal conductivity of approximately 215 W mK-1 at room temperature, significantly lower than that of pristine graphene. This decrease is due to characteristic phonon scattering within Irida-G's porous structure. Additionally, the phonon group velocities and vibrational density of states for Irida-G were analyzed, revealing reduced average phonon group velocities compared to graphene. The thermal conductivity of Irida-G is isotropic and shows significant size effects, transitioning from ballistic to diffusive heat transport regimes as the system length increases. These results suggest that while Irida-G has lower thermal conductivity than graphene, it still holds potential for specific thermal management applications, sharing characteristics with other two-dimensional materials.

TH-graphyne: a new porous bidimensional carbon allotrope.

Graphyne and two-dimensional porous carbon-based materials have garnered significant attention due to their interesting structural characteristics and essential properties for new technological applications. Within this scope, this work investigates the structural, thermal, electronic, optical, and mechanical properties of a novel two-dimensional allotrope that combines triangular (T) and hexagonal (H) rings, connected by acetylenic linkages (graphyne-like), thus named TH-graphyne (TH-GY). This study comprehensively characterizes the proposed system's behavior using density functional theory, ab initio molecular dynamics, and classical reactive molecular dynamics simulations. Our results confirm the structural stability of TH-GY. AIMD simulations demonstrate the material's thermal stability at elevated temperatures, while phonon dispersions indicate its dynamical stability. Electronic band structure calculations show that the system is metallic. The analysis of optical properties reveals intense activity in the visible and UV regions, with pronounced anisotropy. A machine learning interatomic potentials model was developed for TH-GY and used to determine the mechanical behavior of the system, which exhibits Young's modulus ranging from 263 to 356 GPa, highlighting its flexibility. Classical reactive MD simulations elucidate the fracture behavior of TH-GY, revealing distinct fracture patterns and mechanical anisotropy.

Proposing TODD-graphene as a novel porous 2D carbon allotrope designed for superior lithium-ion battery efficiency.

The category of 2D carbon allotropes has gained considerable interest due to its outstanding optoelectronic and mechanical characteristics, which are crucial for various device applications, including energy storage. This study uses density functional theory calculations, ab initio molecular dynamics (AIMD), and classical reactive molecular dynamics (MD) simulations to introduce TODD-Graphene, an innovative 2D planar carbon allotrope with a distinctive porous arrangement comprising 3-8-10-12 carbon rings. TODD-G exhibits intrinsic metallic properties with a low formation energy and stability in thermal and mechanical behavior. Calculations indicate a substantial theoretical capacity for adsorbing Li atoms, revealing a low average diffusion barrier of 0.83eV. The metallic framework boasts excellent conductivity and positioning TODD-G as an active layer for superior lithium-ion battery efficiency. Charge carrier mobility calculations for electrons and holes in TODD-G surpass those of graphene. Classical reactive MD simulation results affirm its structural integrity, maintaining stability without bond reconstructions at 2200K.

Mechanical, Electronic, and Optical Properties of 8-16-4 Graphyne: A 2D Carbon Allotrope with Dirac Cones

Graphene’s success has led to the theoretical prediction and experimental synthesis of various 2D carbon-based allotropes. To explore the mechanical, structural, electronic, and optical properties of 8-16-4 graphyne, we employed density functional theory using the GGA/PBE approach, ab initio molecular dynamics (AIMD), and classical reactive molecular dynamics simulations. Our AIMD results indicate that this material demonstrates excellent dynamical and thermal stabilities. It has a formation energy of −8.57 eV/atom and an elastic moduli of 262.37 GPa. Regarding its band structure, this graphyne analogue is a semimetal with two Dirac cones. It also exhibits transparency and intense optical activity in the infrared region. Notably, the band structure of 8-16-4 graphyne remains practically unchanged at moderate strain regimes. To our knowledge, this is the first known 2D carbon allotrope to exhibit such behavior.

(Invited) Role of the Electrolyte on Li Cation Electrodeposition and Intercalation

Cation transport through the electrolyte to the anode is one most important steps to understand desolvation and diffusion through the electrolyte phase To help understanding this step, there is a sustained development of sophisticated in situ surface science and electrochemical techniques, and first-principles based computational methods. In this work, we analyze the structure and dynamics of state-of-the-art electrolytes particularly at interfaces of typical intercalation anodes. We use classical reactive molecular dynamics and ab initio molecular dynamics to characterize the interfacial systems, and constrained molecular dynamics to investigate the role of highly structured solvation structures on cation deposition and intercalation.

Evaluation of nanocellulose interaction with water pollutants using nanocellulose colloidal probes and molecular dynamic simulations

Atomic Force Microscope (AFM) probes were successfully functionalized with two types of nanocellulose, namely 2,2,6,6-tetramethylpiperidine-1-oxylradical (TEMPO)-mediated oxidized cellulose nanofibers (TOCNF) and cellulose nanocrystals (CNC) and used to study interfacial interactions of nanocellulose with Cu(II) ions and the Victoria blue B dye in liquid medium. TOCNF modified tip showed higher adhesion force due to adsorption of Cu(II) ions and dye molecules compared to CNC ones. Exploring the adsorption properties through classical reactive molecular dynamics simulations (ReaxFF) at the atomic scale confirmed that the Cu(II) ions promptly migrated and adsorbed onto the nanocelluloses through the co-operative chelating action of carboxyl and hydroxyl species. The adsorbed Cu(II) ions showed the tendency to self-organize by forming nano-clusters of variable size, whereas the dye adopted a flat orientation to maximize its adsorption. The satisfactory agreement between the two techniques suggests that functionalized AFM probes can be successfully used to study nanocellulose surface interactions in dry or aqueous environment.

Experimental and theoretical elucidation of catalytic pathways in TiO2-initiated prebiotic polymerization.

The tendency of glycine to form polymer chains on a rutile(110) surface under wet/dry conditions (dry-wet cycles at high temperature) is studied through a conjunction of surface sensitive experimental techniques and sequential periodic multilevel calculations that mimics the experimental procedures with models of decreasing complexity and increasing accuracy. X-ray photoemission spectroscopy (XPS) and thermal desorption spectroscopy (TDS) experimentally confirmed that the dry-wet cycles lead to Gly polymerization on the oxide support. This was supported by all the theoretical characterizations. First, classical reactive molecular dynamics (MD) simulations based on the ReaxFF approach were used to reproduce the adsorption of the experimental glycine solution droplets sprayed onto an oxide support and to identify the most probable arrangement of the molecules that triggered the polymerization mechanisms. Then, quantum chemistry density functional tight binding (DF-TB) MDs and static density functional theory (DFT) calculations were carried out to further explore favorable configurations and to evaluate the energy barriers of the most promising reaction pathways for the peptide bond-formation reactions. The results confirmed the fundamental role played by the substrate to thermodynamically and kinetically favor the process and disclosed its main function as an immobilizing agent: the molecules accommodated in the surface channels close to each other were the ones starting the key events of the dimerization process and the most favorable mechanism was the one where a water molecule acted as a proton exchange mediator in the condensation process.

Formation of Multilayer Graphene Domains with Strong Sulfur-Carbon Interaction and Enhanced Sulfur Reduction Zones for Lithium-Sulfur Battery Cathodes.

A newly designed sulfur/graphene computational model emulates the electrochemical behavior of a Li-S battery cathode, promoting the S-C interaction through the edges of graphene sheets. A random mixture of eight-membered sulfur rings mixed with small graphene sheets is simulated at 64 wt %sulfur loading. Structural stabilization and sulfur reduction calculations are performed with classical reactive molecular dynamics. This methodology allowed the collective behavior of the sulfur and graphene structures to be accounted for. The sulfur encapsulation induces ring opening and the sulfur phase evolves into a distribution of small chain-like structures interacting with C through the graphene edges. This new arrangement of the sulfur phase not only leads to a less pronounced volume expansion during sulfur reduction but also to a different discharge voltage profile, in qualitative agreement with earlier reports on sulfur encapsulation in microporous carbon structures. The Li2 S phase grows around ensembles of parallel graphene nanosheets during sulfur reduction. No diffusion of sulfur or lithium between graphene nanosheets is observed, and extended Li2 S domains bridging the space between carbon ensembles are suppressed. The results emphasize the importance of morphology on the electrochemical performance of the composite material. The sulfur/graphene model outlined here provides new understanding of the graphene effects on the sulfur reduction behavior and the role that van der Waals interactions may play in promoting formation of multilayer graphene ensembles and small Li2 S domains during sulfur reduction.

Parametrization of a Reactive Force Field (ReaxFF) for Molecular Dynamics Simulations of Si Nanoparticles.

A novel computational approach, based on classical reactive molecular dynamics simulations (RMD) and quantum chemistry (QC) global energy optimizations, is proposed for modeling large Si nanoparticles. The force field parameters, which can describe bond breaking and formation, are derived by reproducing energetic and structural properties of a set of Si clusters increasing in size. These reference models are obtained through a new protocol based on a joint high temperature RMD/low temperature Basin Hopping QC search. The different procedures of estimating optimal force field parameters and their performance are discussed in detail.

Metal-nanotube composites as radiation resistant materials

The improvement of radiation resistance in nanocomposite materials is investigated by means of classical reactive molecular dynamics simulations. In particular, we study the influence of carbon nanotubes (CNTs) in an Ni matrix on the trapping and possible outgassing of He. When CNTs are defect-free, He atoms diffuse alongside CNT walls and, although there is He accumulation at the metal-CNT interface, no He trespassing of the CNT wall is observed, which is consistent with the lack of permeability of a perfect graphene sheet. However, when vacancies are introduced to mimic radiation-induced defects, He atoms penetrate CNTs, which play the role of nano-chimneys, allowing He atoms to escape the damaged zone and reduce bubble formation in the matrix. Consequently, composites made of CNTs inside metals are likely to display improved radiation resistance, particularly when radiation damage is related to swelling and He-induced embrittlement.

Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations.

The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine molecules in water solution is simulated through classical reactive molecular dynamics simulations based on an accurately parametrized force field. The adsorption modes of the molecules are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent experimental and theoretical data and confirm previous findings for a similar system. The covalent attachments of the molecules to the gold support are all slow physisorptions followed by fast chemisorptions. However, a great variety of binding arrangements can be observed. Interactions with the adsorbate caused surface modulations in terms of adatoms and dislocations which contributed to strengthen the cysteine adsorption.

Lithium ion solvation and diffusion in bulk organic electrolytes from first-principles and classical reactive molecular dynamics.

Lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF6(-) anion. Li(+) prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li(+) solvation. Corresponding analysis for the PF6(-) anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. These results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.

Classical Reactive Molecular Dynamics Implementations: State of the Art

Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material-specific coarse-grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many-body or bond-order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi-empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car-Parinello molecular dynamics.

A Reactive Molecular Dynamics Study of the Thermal Decomposition of Perfluorodimethyl Ether

Classical reactive molecular dynamics (RMD) simulation is used to model the thermal decomposition of perfluorodimethyl ether (CF(3)OCF(3)), which is relevant as a simple molecule containing the necessary architectural elements to study the chemical stability of perfluoropolyether lubricants. The RMD algorithm employs nonreactive interaction potentials for the reactants and products. The reactivity is implemented through a coarse-grained simulation algorithm, incorporating elements from both the quantum and macroscopic descriptions of the reaction. The RMD scheme maps the quantum mechanically determined transition state onto a set of geometric triggers. When a configuration matching those triggers is found in the RMD simulation, the reaction instantaneously occurs. A brief, local equilibration process stabilizes the configuration, and the simulation continues. Using two geometric triggers, the RMD simulation can describe quantitatively the temperature dependence of the thermal decomposition of CF(3)OCF(3), when compared to the quantum mechanical standard.