Nashrieh Shimi va Mohandesi Shimi Iran

Nashrieh Shimi va Mohandesi Shimi Iran

ReaxFF Force Field in Molecular Dynamic Simulation of Reactive Systems

Document Type : Review Article

Authors
Mohammad Ebrahim Izadi
Hassan Sabzyan
Department of Chemistry, University of Isfahan, Isfahan, I.R. Iran
Abstract
 In this review article, the potential functions of the reactive force field ReaxFF used in reactive molecular dynamics (RMD) simulations are introduced and described. This force field with its special potential functions is used to simulate chemical reaction systems with accuracies close to those of quantum chemical calculations within reasonable computation times, even with about one million atoms on high-performance computing facilities. Variations of the partial charges of atoms during chemical reactions can also be calculated and probed within RMD simulations with accuracies very close to those calculated by density functional methods. In addition to the general potential functions incorporated in non-reactive force fields, in ReaxFF force field, there are a number of special (usually complex) potential functions describing details of the bonding structures and charge states of atoms in different coordination states and chemical and solvent environments. All of these potential functions are described in this paper, and examples are calculated and plotted to demonstrate clearly their behavior and their corresponding chemical and physical backgrounds. Finally, important evolutions of the ReaxFF force field and a few of its applications have been presented.
Keywords
Reactive Molecular Dynamic (RMD) Simulation
ReaxFF force field
Bonding potential function
Non-bonding interactions
Chemical reaction system

Subjects

[1] van Duin A.C.T., Goddard III W.A., Dasgupta S., ReaxFF: a Reactive Force Field for Hydrocarbons, J. Phys. Chem. A, 41(105): 9396–9409 (2001).
[2] Chenoweth K., van Duin A.C.T., Goddard III W.A., ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation, J. Phys. Chem. A, 5(112): 1040-1053 (2008).
[3] van Duin A.C.T., Goddard III W.A., Strachan A., Stewman S., Zhang Q., Xu X., ReaxFFsio Reactive Force Field for Silicon and Silicon Oxide Systems, J. Phys. Chem. A, 19(107): 3803-3811 (2003).
[4] Fogarty J.C., Aktulga H.M., Grama A.Y., van Duin A.C.T., Pandit S.A., A Reactive Molecular Dynamics Simulation of the Silica-Water Interface, J. Chem. Phys., 17(132): 174704-174714 (2010).
[5] van Duin A.C.T., Goddard III W.A., Strachan A., Chakraborty D., Dasgupta D., Shock Waves in High-Energy Materials: the Initial Chemical Events in Nitramine RDX, Phys. Rev. Lett., 9(91): 7-10 (2003).
[6] van Duin A.C.T., Goddard III W.A., Strachan A., Kober E.M., Oxgaard J., Thermal Decomposition of RDX from Reactive Molecular Dynamics, J. Chem. Phys., 5(122): 54502-54512 (2005).
[7] Neyts E.C., van Duin A.C.T., Bogaerts A., Insights in the Plasma-Assisted Growth of Carbon Nanotubes Through Atomic Scale Simulations: Effect of Electric Field, J. Am. Chem. Soc., (134): 1256-1260 (2012).
[8] Chaban V.V., Fileti E.E., Prezhdo O.V., Buckybomb: Reactive Molecular Dynamics Simulation, J. Phys. Chem. Lett., 5(6): 913-917 (2015).
[9] Srinivasan S.G., van Duin A.C.T., Ganesh P., Development of a Reaxff Potential for Carbon Condensed Phases and Its Application to the Thermal Fragmentation of a Large Fullerene, J. Phys. Chem. A, 4(119): 571-580 (2015).
[10] Ostadhossein A., Rahnamoun A., Wang Y., Zhao P., Zhang S., Crespi V.H., van Duin A.C.T., ReaxFF Reactive Force-Field Study of Molybdenum Disulfide (MoS2), J. Phys. Chem. Lett., 3(8): 631-640 (2017).
[11] Shin Y.K., Gai L., Raman S., van Duin A.C.T., Development of a ReaxFF Reactive Force Field for the Pt-Ni Alloy Catalyst, J. Phys. Chem. A, 41(120): 8044–8055 (2016).
[12] Hong S., van Duin A.C.T., Atomistic-Scale Analysis of Carbon Coating and Its Effect on the Oxidation of Aluminum Nanoparticles by Reaxff-Molecular Dynamics Simulations, J. Phys. Chem. C, 17(120): 9464–9474 (2016).
[13] Huygh S., Bogaerts A., van Duin A.C.T., Neyts E.C., Development of a Reaxff Reactive Force Field for Intrinsic Point Defects in Titanium Dioxide, Comput. Mater. Sci., (95): 579-591 (2014).
[14] Raymand D., van Duin A.C.T., Baudin M., Hermansson K., A Reactive Force Field (ReaxFF) for Zinc Oxide, Surf. Sci., 5(602): 1020-1031 (2008). 
[15] Monti S., Corozzi A., Fristrup P., Joshi K.L., Shin Y.K., Oelschlaeger P., van Duin A.C.T., Barone V., Exploring the Conformational and Reactive Dynamics of Biomolecules in Solution Using an Extended Version of the Glycine Reactive Force Field, Phys. Chem. Chem. Phys., 36(15): 15062-15077 (2013).
[16] Rahaman O., van Duin A.C.T., Goddard III W.A., Doren D.J., Development of a ReaxFF Reactive Force Field for Glycine and Application to Solvent Effect and Tautomerization, J. Phys. Chem. B, 2(115): 249–261 (2011).
[17] Abolfath R.M., van Duin A.C.T., Brabec T., Reactive Molecular Dynamics Study on the First Steps of DNA-Damage by Free Hydroxyl Radicals, J. Phys. Chem. A, 40(115): 11045–11049 (2011).
[18] Rahaman O., van Duin A.C.T., Bryantsev V.S., Mueller J.E., Solares S.D., Goddard III W.A., Doren D.J., Development of a ReaxFF Reactive Force Field for Aqueous Chloride and Copper Chloride, J. Phys. Chem. A, 10(114): 3556–3568 (2010).
[19] Zhang W., van Duin A.C.T., Second-Generation Reaxff Water Force Field: Improvements in the Description of Water Density and OH-Anion Diffusion, J. Phys. Chem. B, 24(121): 6021-6032 (2017).
[20] Mortier W.J., Ghosh S.K., Shankar S., Electronegativity Equalization Method for the Calculation of Atomic Charges in Molecules, J. Am. Chem. Soc., 15(108): 4315-4320 (1986).
[21] Senftle T.P., Hong S., Islam M.M., Kylasa S.B., Zheng Y., Shin Y.K., Junkermeier C., The ReaxFF Reactive Force-Field: Development, Applications and Future Directions, npj Comput. Mater., 1(2): 15011-15025 (2016).
[22] Goddard III W.A., Chenoweth K., Pudar S., van Duin A.C.T., Cheng M.J., Structures, Mechanisms, and Kinetics of Selective Ammoxidation and Oxidation of Propane Over Multi-Metal Oxide Catalysts, Top. Catal., 4(50): 2-18 (2008).
[23] Chenoweth K., van Duin A.C.T., Goddard III W.A., The ReaxFF Montecarlo Reactive Dynamics Method for Predicting Atomistic Structures of Disordered Ceramics: Application to the Mo3VOx Catalyst, Angew. Chem. Int. Ed., 41(48): 7630–7634 (2009).
[24] Vasenkov A., Newsome D., Verners O., Russo M.F., Zaharieva R., van Duin A.C.T., Reactive Molecular Dynamics Study of Mo-Based Alloys Under High-Pressure, High-Temperature Conditions, J. Appl. Phys., 1(112): 13511-13524 (2012).
[25] Kamat A.M., van Duin A.C.T., Yakovlev A., Molecular Dynamics Simulations of Laser-Induced Incandescence of Soot Using an Extended Reaxff Reactive Force Field, J. Phys. Chem. A, 48(114): 12561–12572 (2010).
[26] Castro-Marcano F., Kamat A.M., Russo M.F., van Duin, A.C.T., Mathews J.P., Combustion of an Illinois No. 6 coal Char Simulated Using an Atomistic Char Representation and the ReaxFF Reactive Force Field, Combust. Flame, 3(159): 1272-1285 (2011).
[27] Weismiller M.R., van Duin A.C.T., Lee J., Yetter R.A., ReaxFF Reactive Force Field Development and Applications for Molecular Dynamics Simulations of Ammonia Borane Dehydrogenation and Combustion, J. Phys. Chem. A, 17(114): 5485–5492 (2010).
[28] Mueller J.E., van Duin A.C.T., Goddard III W.A., Application of the ReaxFF Reactive Force Field to Reactive Dynamics of Hydrocarbon Chemisorption and Decomposition, J. Phys. Chem. C, 12(114): 5675–5685 (2010).
[29] Agrawalla S., van Duin A.C.T., Development and Application of a ReaxFF Reactive Force Field for Hydrogen Combustion, J. Phys. Chem. A, 6(115): 960–972 (2011).
[30] Pitman M.C., van Duin A.C.T., Dynamics of Confined Reactive Water in Smectite Clay-Zeolite Composites, J. Am. Chem. Soc., 6(134): 3042–3053 (2012).
[31] Manzano H., Moeini S., Marinelli F., van Duin A.C.T., Ulm F. J., Pellenq R.J.M., Confined Water Dissociation in Microporous Defective Silicates: Mechanism, Dipole Distribution, and Impact on Substrate Properties, J. Am. Chem. Soc., 4(134): 2208–2215 (2012).
[32] van Duin A.C.T., Bryantsevb V.S., Diallob M.S., Goddard III W.A., Rahamanc O., Dorenc D.J., Raymandd D., Hermanssond K., Development and Validation of a ReaxFF Reactive Force Field for Cu-Cation/Water Interactions and Copper Metal/Metal Oxide/Metal Hydroxide Condensed Phases, J. Phys. Chem. A, 35(114): 9507–9514 (2010).
[33] https://scifinder.cas.org
[34] Chenoweth K., van Duin A.C.T., Cheung S., Goddard III W.A., Kober E.M., Simulations on the Thermal Decomposition of a Poly(Dimethylsiloxane) Polymer Using the ReaxFF Reactive Force Field, J. Am. Chem. Soc., 19(127): 7192–7202 (2005).
[35] Ashraf C., Jain A., Xuan Y., van Duin A.C.T., ReaxFF Based Molecular Dynamics Simulations of Ignition front Propagation in Hydrocarbon/Oxygen Mixtures Under High Temperature and Pressure Conditions, Phys. Chem. Chem. Phys., 19: 5004-5017 (2017).
[36] Ashraf C., van Duin A.C.T., Extension of the ReaxFF Combustion Force Field Toward Syngas Combustion and Initial Oxidation Kinetics, J. Phys. Chem. A, 5(121): 1051–1068, (2017).
[37] Chen Z., Sun W., Zhao L., High-Temperature and High-Pressure Pyrolysis of Hexadecane: A Molecular Dynamic Simulation Based on Reactive Force Field (ReaxFF), J. Phys. Chem. A, 10(121): 2069–2078, (2017).
[38] Lotfi R., van Duin A.C.T., Biswas M.M., Molecular Dynamics Simulations of Perfluoropolyether Lubricant Degradation in the Presence of Oxygen, Water, and Oxide Nanoparticles Using a ReaxFF Reactive Force Field, J. Phys. Chem. C, 5(122): 2684–2695, (2018).
[39] Islam M.M., Strachan A., Decomposition and Reaction of Polyvinyl Nitrate Under Shock and Thermal Loading: a ReaxFF Reactive Molecular Dynamics Study, J. Phys. Chem. C, 40(121): 22452–22464, (2017).
[40] Yeo B.C., Jung H., Lee H.W., Yun K.S., Kim H., Lee K.R., Han S.S., Atomistic Simulation Protocol for Improved Design of Si−O−C Hybrid Nanostructures as Li-ion Battery Anodes: ReaxFF Reactive Force Field, J. Phys. Chem. C, 42(121): 23268–23275, (2017).
[41] Han S., Li X., Nie F., Zheng M., Liu X., Guo L., Revealing the Initial Chemistry of Soot Nanoparticle Formation by ReaxFF Molecular Dynamics Simulations, Energy Fuels., 8(31): 8434–8444, (2017).
[42] Galiullina G.M., Orekhov N.D., Stegailov V.V., Nanostructures Nucleation in Carbon–Metal Gaseous Phase: a Molecular Dynamics Study, J. Phys.: Conf. Ser., 1(946): 12110–12118, (2018).
[43] Hong S., Sheng C., Krishnamoorthy A., Rajak P., Tiwari S., Nomura K., Misawa M., Shimojo F., Kalia R.K., Nakano A., Vashishta P., Chemical Vapor Deposition Synthesis of MoS2 Layers from the Direct Sulfidation of MoO3 Surfaces Using Reactive Molecular Dynamics Simulations, J. Phys. Chem. A, 3(121): 7494–7503, (2018).
[44] Hong S., Sheng C., Krishnamoorthy A., Kalia R.K., Nakano A., Vashishta P., A Reactive Molecular Dynamics Study of Atomistic Mechanisms During Synthesis of MoS2 Layers by Chemical Vapor Deposition, Adv. Mater. Res., 5(6): 307–311, (2018).
[45] Zeng H., Cheng X., Zhang C.Y., Lu Z.P., Responses of Core-Shell Al/Al2O3 Nanoparticles to Heating: ReaxFF-Molecular Dynamics Simulations, J. Phys. Chem. C, 16(122): 9191–9197, (2018).
[46] Cagin T., Tigli A., A case study on Metal-Ceramic Interfaces: Wetting of Alumina by Molten Aluminum, Mater. Sci. Forum, (915): 185–189, (2018).
[47] Yeon J., He X., Martini A., Kim S.H., Mechanochemistry at Solid Surfaces: Polymerization of Adsorbed Molecules by Mechanical Shear at Tribological Interfaces, Appl. Mater. Interfaces, 3(9): 3142–3148, (2017).
[48] Sun Y., Liu Y., Chen X., Zhai Z., Xu F., Liu Y., Micromechanism of Oxygen Transport During Initial Stage Oxidation in Si (100) Surface: a ReaxFF Molecular Dynamics Simulation Study, Appl. Surf. Sci., 5(406): 178–185, (2017).
[49] Zhu R., Janetzko F., Zhang Y., van Duin A.C.T., Goddard III W.A., Salahub D.R., Characterization of the Active Site of Yeast RNA Polymerase II by DFT and ReaxFF Calculations, Theor. Chem. Acc., 4(120): 479–489, (2008).
[50] Monti S., van Duin A.C.T., Kim S.Y., Barone V., Exploration of the Conformational and Reactive Dynamics of Glycine and Diglycine on TiO2: Computational Investigations in the Gas Phase and in Solution, J. Phys. Chem. C, 8(116): 5141–5150, (2012).
[51] Monti S., Corozzi A., Fristrup P., Joshi K.L., Shin Y.K., Oelschlaeger P., van Duin A.C.T., Barone V., Exploring the Conformational and Reactive Dynamics of Biomolecules in Solution Using an Extended Version of the Glycine Reactive Force Field, Phys. Chem. Chem. Phys., 36(15): 15062–15077, (2013).
[52] Keten S., Chou C.C., van Duin A.C.T., Buehler M.J., Tunable Nanomechanics of Protein Disulfde Bonds in Redox Microenvironments, J. Mech. Behav. Biomed Mater., 1(5): 32–40, (2017).
[53] Majidi R., Mansouri K., Molecular Dynamics Simulation of Oxygen and Nitrogen Mixture on Carbon Nanocone and Nanotube, Nashrieh Shimi va Mohandesi Shimi Iran (NSMSI), 36(2): 133-141, (2017).
[54] Kariminiya H., Farhadi F., Simulation and Techno-Economic Investigation of Solar Assisted Single-Effect Water-Lithium Bromide Absorption Chiller, Nashrieh Shimi va Mohandesi Shimi Iran (NSMSI), 33(3): 53-64, (2014).
[55] Pakdel A., Jafari Nasr M.R., Simulation and Parametric Investigation of Combined Parabolic Through Collector (PTC) and Organic Rankine Cycle (ORC), Nashrieh Shimi va Mohandesi Shimi Iran (NSMSI), 33(3): 65-83, (2014).
[56] Ghaemi A., Shahhosseini S., Ghannadi Maragheh M., Experimental Investigation of Reactive Absorption of Ammonia and Carbon Dioxide by Carbonated Ammonia Solution, Iran. J. Chem. Chem. Eng(IJCCE)., 30(2): 43-50, (2011).
[57] Zeini-Isfahani A., Roberts M.W., Carley A.F., Read S., The Reactive Chemisorption of Carbon Dioxide at Mg(100) Surface, Iran. J. Chem. Chem. Eng(IJCCE)., 13(1): 25-29, (1994).