Reactive force-field molecular dynamics

Goddard et al. developed and validated the reactive force field (ReaxFF) to describe complex reactions (including catalysis) nearly as accurately as QM in some cases but at computational effort comparable to classical molecular dynamics (MD).10,18 Similar to empirical non-reactive force fields, the reactive force field divides the system energy up into various partial energy contributions,... 

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 . 

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. 

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. 

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... 

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. 

Russo, M., Li, R., Mench, M., and van Duin, A.C.T. Molecular dynamic simulation of aluminum-water reactions using the ReaxFF reactive force field. International Journal of Hydrogen Energy, 36, 5828-5835, 2011. 

Of particular interest in this work is the use of ab initio data sets to fit empirical potential parameters to be used in molecular dynamics (MD) simulations. ReaxFF is a transferable reactive force field designed by van Duin et al. [6] to cover a wide range of elements in the periodic table including very successful predictions of a variety of hydrocarbon molecular structures. ReaxFF was also developed for boron/ nitrogen/hydrogen [7], silicon/silica systems [8], and transition metal complexes [9]... 

The results of molecular dynamics simulations are critically dependent on the quality of the force field. In principle, any potential that accurately describes SWNT should have terms that reflect the curvature of the tube. However, curvature effects are largely ignored in force fields published in the literature.20-23 Some potentials, such as those based on reactive bond-order formalism, correctly account for the local curvature in describing the covalent bonding interactions.24-26 But the adsorption... 

The process of adsorption and interaction of probe molecules such as ammonia, carbon monoxide as well as the whole spectrum of organic reactant molecules with zeolite catalysts has been the subject of numerous experimental and computational studies. These interaction processes are studied using several computational methods involving force fields (Monte Carlo, molecular dynamics emd energy minimization) or quantum chemical methods. Another paper [1] discusses the application of force field methods for studying several problems in zeolite chemistry. Theoretical quantum chemical studies on cluster models of zeolites help us to understand the electronic and catalytic properties of zeolite catalysts. Here we present a brief summary of the application of quantum chemical methods to understand the structure and reactivity of zeolites. 

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