Reactive force-field simulations

Reactive Force Field Simulations on Benzene Adsorption on the Raney-Nickel Catalyst... 

Describe the main approaches to the construction of empirical force fields for molecular dynamic simulations. Describe the difference between ordinary and reactive force fields. 

Progress was also reported in modeling the reaction and transportation processes on fuel cell catalysts and through membranes, using multiple paradigms as well as starting from first principle quantum mechanics to train a reactive force field that can be applied for large scale molecular dynamics simulations. It is expected that the model would enable the conception, synthesis, fabrication, characterization, and development of advanced materials and structures for fuel cells . 

Once the bond orders have been calculated, they are used to compute bond energies, angles, and torsions. These terms are also used in non-reactive force fields, but their use in reactive simulations requires some modifications. All covalent terms are pre-multiplied by the bond orders involved this ensures that whenever a bond is broken, all the terms involving it vanish smoothlv. Also, the equilibrium angle in covalent-angle terms depends upon the bond orders... 

Despite this progress several areas require further development. For example, we have evidenced that only a limited number of force fields are presently available for treatment of ionic salts, It will be very beneficial that this gap will be filled and general, transferable sets of force fields for different classes of ionic systems will be available as is the case with other classes of energetic materials such as nitramines systems. We have also pointed out in this chapter that current classical force fields developed for ionic crystals are limited to description of nonreactive processes. Development of reactive force fields such as reactive empirical bond order potentials for the case of ionic systems will represent a major forward step for simulation of reactions and of combustion and denotation processes. 

In addition to the classical force fields above, many other force fields have been developed for small drug molecules or macromolecules. The MM2, MM3, and MM4 force fields were developed by Norman L. Allinger for a broad range of chemicals, and CFF is a family of force fields adapted to a broad variety of organic compounds, polymers, metals, and so on. The MMFF force field was developed at Merck for a broad range of chemicals. ReaxFF is a reactive force field, developed by William Goddard and coworkers, is fast, transferable, and the computational method of choice for atomistic-scale dynamics simulations of chemical reactions. 

The AIMD method, based on the Carr and ParrineUo approach [127], has also been applied in the study of electrochemistry [128]. Reactive Force Field approaches are now being used to study the ionomer/water/catalyst interfaces during an electrochemical reaction [129]. Neurock et al. developed a detailed first-principles approach that employs a double-reference method to simulate the influence of the electrochemical potential on the chemistry at the metal/solution interface [130]. hi this method the aqueous solution metal interface and the interfacial potential drop are explicitly treated. However the choice of an appropriate water surface structure is critical for establishing the appropriate electrochemical behavior at the atomistic scale. This method has been applied to smdy some electrochemical steps involved in the ORR and methanol oxidation on Pt (e.g. [131, 132]). 

Besides electrode surface structure, the nature of the electrode and solvent also affect the evolution of the SEI. An interesting and detailed simulation of formation and growth of SEI on Li metal surface in EC, DMC, and EC mixed with DMC electrolyte was done by Kim et al., using reactive force field (ReaxFF) molecular simulations [61]. The SEI film was found to grow faster in EC-based electrolyte compared to DMC, generating thicker SEI film, and EC mixed with DMC electrolyte came in between, as shown in Fig. 5.18. This simulation result agrees with the... 

By using molecular dynamics with a reactive force field [28-30] as implemented in LAMMPS [31], we were able to analyze the side effects of ion bombardment on a sihca-supported single waUed carbon nanotube. A reactive force field enables simulating the breaking and formation of covalent bonds. Apart from observing the effective removal of carbon atoms, we found the possibility of undesired effects on the carbon nanotube sidewall, on the substrate as well as at the interface between the carbon nanotube and the substrate (Fig. 7.1). We highlight the main types of atomic defect found on carbon nanotube sidewall, vacancy defects and chemisorption. 

In addition to QC studies, reactive molecular dynamics (RMD) simulations using the reactive force field ReaxFF have been used to gain insight into reactions of singly reduced EC in the condensed (solution) phase [31]. In this study the reaction of Li /o-EC with both LiVo-EC and LiVc-EC has been studied in a solution of EC molecules. A snapshot of the system is shown in Fig. 7.5. RMD simulations were used to determine the free energy as a function of reaction coordinate (see below) and to examine the propensity of various radical combination reactions to occur in the condensed phase of an EC solvent. 

Chenoweth K et al (2005) Simulations on the thermal decomposition of a poly(dimethylsi-loxane) polymer using the ReaxEF reactive force field. J Am Chem Soc 127(19) 7192-7202... 

Enabling dynamical simulations on large reacting systems ( 1,000 atoms), so-called reactive force fields have been introduced. An example of such force... 

In associating liquids the molecular dipole moments increase by 40-60% compared to the isolated molecule. These solvents will therefore strongly affect the chemical reactivity of solute molecules. Classical force field simulations neglecting polarization will not be able to capture these changes. 

We note that our model could be improved by introducing a reactive force field also for the metal phase, where the formation of an oxide phase with the correct stoichiometry may be induced. This is because a reactive force field may allow changes of the charges on O and the metal atoms as the oxide reaction is taking place. However, our simulation is a very good approximation that captures many of the qualitative features observed on the surface at the onset of surface oxidation formation. 

Kim SY, Van Duin ACT, Kubicki JD Simulations of the Interactions between Ti02 nanoparticles and water with Na" and Cl, methanol and formic acid using a reactive force field, J Mater Res 28 513-520, 2013. 

The most basic approach to carry out MD simulations for larger systems is to use classical force fields. A variety of different force fields for molecular mechanics (MM) simulations has been developed,which are mainly intended to describe the non-reactive dynamics of large systems. In particular in the field of biochemistry force fields play an essential role to study the complex properties of large biomolecules. However, classical force fields require the specification of the connectivity of the atoms. Therefore, they are not able to describe chemical reactions, i.e., the making and breaking of bonds. To describe reactions, they can be combined with quantum mechanical (QM) methods in so-called QM/MM simulations. In recent years also reactive force fields , e.g. ReaxFF, have been introduced, which overcome this limitation. However, these reactive force fields are typically highly adapted to specific systems by analytic terms customized to describe e.g. certain bonding situations, and only a few applications have been reported so far. 

Mainly in the field of materials science various types of potentials have been developed based on the concept of the bond order. " Like for reactive force fields also for the application of these potentials a specification of the atomic positions is sufficient. Although many of these potentials like the Tersoff potential, the Stillinger-Weber potential, the Breimer potential and many others have been introduced already one or two decades ago, they are still frequently used in materials simulations, in particular for semiconductors. For metallic systems the embedded atom method (EAM) and the modified embedded atom method (MEAM) introduced by Baskes and coworkers are widely distributed. 

Our theoretical investigation regarding the understanding of the conversion of iminium into enamine in the framework of a proline-catalyzed aldol reaction emphasizes that the reactive force field (FF), ReaxFF, used in combination with molecular dynamics (MD) simulations is a relevant method to investigate the mechanism of proton transfers in iminium-enamine conversions. This approach should be extended to model other steps of proline-catalyzed... 

Shen XJ, Xiao Y, Dong W, Yan XH, Busnengo HE (2012) Molecular dynamics simulations based on reactive force-fields for surface chemical reactions. Comput Theor Chem 990 152-158... 

This chapter will focus on the modeling of MEA and its polymer electrolyte membrane. First, 3D modeling of PEMFC and its MEA will be discussed, and an example will be put forward. Then, dynamic modeling of PEM will be introduced. Further, this chapter will move on to the fault-embedded modeling of PEM. As an extension, application of membranes in other cases will be recommended, such as in lithium battery, vanadium redox flow battery (VRFB), chlor-alkali electrolysis, water electrolysis, and solar cell. Finally, several typical examples will be given, including Pt and Pt alloy simulation with density functional theory (DFT), water formation and Pt adsorption on carbon reactive force field (ReaxFF) simulation, and coarse-grained simulations. 

Computer experiments particularly use quantum chemical approaches that provide accurate result with intense computational cost. Classical or semiempirical methods on the other hand are able to simulate thousands or up to millions of atoms of a system with pairwise Lennard-Jones (LJ)-type potentials [104-107]. Thus, LJ-type potentials are very accurate for inert gas systems [108], whereas they are unable to describe reactions or they do so by predetermined reactive sites within the molecules of the reactive system [109]. van Duin and coworkers [109-115] developed bond-order-dependent reactive force field technique is called ReaxFF as a solution to the aforementioned problems. Therefore, ReaxFF force field is intended to simulate reactions. They are successfully implemented to study hydrocarbon combustion [112,115,116] that is based on C-H-0 combustion parameters, fuel cell [110,111], metal oxides [117-122], proteins [123,124], phosphates [125,126], and catalyst surface reactions and nanotubes [110-113] based on ReaxFF water parameters [127]. Bond order is the number of chemical bonds between a pair of atoms that depends only on the number and relative positions of other atoms that they interact with [127]. Parameterization of ReaxFFs is achieved using experimental and quantum mechanical data. Therefore, ReaxFF calculations are fairly accurate and robust. The total energy of the molecule is calculated as the combination of bonded and nonbonded interaction energies. 

Chenoweth, K., van Duin, A.C.T., and Goddard III, W.A. ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation. Journal of Physical Chemistry A, 112,1040-1053, 2008. 

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