Journal ArticleReaction pathways for polyaromatic growth in combustion environments are explored theoretically using molecular dynamic techniques. The reaction systems considered include cyclization reactions that involve H atom migration. Specifically we examine the absorption of acetylene on an aromatic ring radical. The Parallel Replica method for accelerating Molecular Dynamics calculations is used to screen reaction pathways. The information obtained through the use of Molecular Dynamics runs are then analyzed with  quantum chemical methods and thermodynamic data for the key compounds

Violi, A.

Voth, Gregory Alan

English

The University of Utah: J. Willard Marriott Digital Library

Identification of Pathways for Polyaromatic Growth Using Molecular Dynamics A. Viol(l, M. Curna 2, G.A. Voth3, A.F. Sarofim1 1 Dept. Chemical and Fuels Engineering 2 Henry Eyring Center for Theoretical Chemistry, Department of Chemistry 3 Center for High Performance Computing University of Utah Salt Lake City UT 84112 Abstract Reaction pathways for polyaromatic growth in combustion environments are explored theoretically using molecular dynamic techniqucs. The reaction systems considered include cyclization reactions that involve H atom migration. Specifically we examine thc absorption of acetylene on an aromatic ring radical. The Parallel Replica method for accelerating Molecular Dynamics calculations is used to screen reaction pathways. The infonnation obtained through the usc of Molecular Dynamics runs are then analyzed with quantum chemical methods and thern10dynamic data for the key compounds. Introduction Polycyclic aromatic hydrocarbons play an important role in the formation of combustion generated particles such as soot, and their presence in atmospheric aerosols has becn widely shown [1]. F ormation and growth of aromatic species bridges the main combustion zone chcmistry with soot formation. The role and the fOlmation mechanism of polycyclic aromatic hydrocarbons in a variety of high temperature phenomena have recently received great attention. Theoretical investigations conducted by Frenklach and co-workers revealed new reaction pathways for aromatic ring growth [2-3], such as enhanced fOlmation of five-, and six-mcmbercd aromatic rings, interconversion of five and six-member rings and migration of the cyclopenta ring along the zig-zag aromatic edges. All these pathways are induced or assisted by hydrogen migration. Unimolecular migration of hydrogen atoms is an important feature of hydrocarbon chemistry [4]. In many of those cases, migration of hydrogen becomes competitive, as compared with a gaseous analog because of molecular rigidity and atomic constraints imposed by the surface. Some examples of hydrogen migration may include dimerization of propargyl [5-6] and cyclopentadicnyl [7] radicals, allene-propyne isomerization [8]. Motivated by the importance of these reactions, we illustrate in this paper the use of Molecular Dynamics (MD) for the study of the reaction pathways for six-member ring eyclization. Molecular Dynamics offers the * Corresponding author: violi@eng.utah.edu Associated Web site: http://combustion.utah.edul advantage of modeling complex systems and not requiring advanced knowledge of the available pathways. In this study we use an accelerated dynamics method in which the system trajectory caught in his current state is stimulated to find an appropriate path for escape more quickly than it would with direct Molecular Dynamics. The present theoretical investigation focus on the application of a molecular dynamics methodology to combustion related problems. The main trust of this paper is to illustrate the application of the method for purposes of evaluating alternative pathways for the cyclization reactions. Specifically we examine hydrogen migration during acetylene absorption on an aromatic ring radical. The escape events identified by running MD on the system are then analyzed using semiempirical quantum methods to calculate the thermodynamic properties ofthe key compounds. After summarizing in the following section the methodological details of thc computations pcrfOlmed, results from the quantum chemical calculations for the pathways identified during MD runs are reportcd. Theoretical Approach Molecular Dynamics in which one chooses an appropriate interatomic potential to describe the forces between atoms and then integrates the classical equation of motion, is the most direct approach among atomistic simulations. Transition state theory can be employed to compute the rate constants provided the dividing surface of the Proceedings of the Third Joint Meeting of the U.S. Sections of The Combustion Institute reaction is known. However, all the possible escape mechanisms cannot be guessed in advance. The underlying mechanisms may be too numerous, too complicated, andlor have an interplay whose consequences are unpredictable. With the approach proposed, as in MD, no a priori infomlution about what Ihis escape path might look like is imposed on the procedure; the trajectory simply finds its own way OUI of the state. With MD, the limitation in the accessible simulation time represents a substantial obstacle in making useful predictions. Resolving individual atomie vibrations requires a femtosecond time step in the integration of the equations of motion, so simulation of reaction mcthanisms on microsecond or larger lime scale is still very difficult even for small systems. For circumventing this time scale problem. we employed one of the methods developed by Voter and co-worker to accelerate dynamics. the Parallel Replica Molecular Dynamics (PRMOl [9J. Among accelerated dynlltnic methods, thc PRMD flOl is the simplest and most accurate method. Stan ing with a N-atom system in a panicular state the entire system is replicated on each of M available parallel processors. After a dephasing stage each processor carries out an independent MD trajcctory for the ent ire N-atom system thus exploring phase space within the panicular basin M times faster than a single trnjectory would. Whenever a transition state is detctted all processors are alened to stop. The simulation clock is advanced Thc potelltial used for these si mulations is the empirical bond-order potcntials of Brenner [II J, which is able to capture many of the essential features of chemical bonding in hydrocarbons. TcrsolT had previously proposed eOcctive many body empirical potential for all group I V clements in which the potential encrgy of the system is wrinen as a sum of cffective pair tcnns for each bond, the cnergetics of which depends on the local environment. These potentials are very accurate for Si and Ge but less reliable for C [12]. [n fact, the Tersoff potential for CO which has been fit to the bulk propenics of both diamond and graphite, docs not distinguish the chcmical charaetcr of the bond. This shoneomillg tums out to bc particularly serious when dealing wi th structures prcsenting both types of bonding. Brenner [II} has re-parametrized the Tersoff potential and added non local tenns to properly account for the bond modilications induced by a change of bonding of neighboring atoms. The major improvement with respect to Tersoff is due to the fa ct that Ihe bond energy takes into account the local environment via a many body ternl which depends not only on bond length and angle but also on the coordination of the atoms making the bond and of their nearest neighbor. Petukhov et al. have demonstrated the high accuracy of the 2 empirical many-body Brenner potential [or carbon struclllres by a detailed comparison of its structures by a detailed comparison of its structural predictions with those of ab-illilio studies for known reconstruction of diamond (100) and ( III ) surfaecs [13]. Results Surface growth of carbonaceous material is proposed to follow sequential hydrogen abstraction that creatcs a surface radical, acetylene addition to the radical fonned, and ring eyclization. This reaction pathway is here studied using Parallel Rcpliea for a system composed of acetylene and 4-phenantryl rndieal. For this small system the input configuration has been replicated on 7 processors. A minimization is pcrfomlcd to generate a reference configuration for transition checks. On each processor aner a momentum randomization stage to eliminate correlations with other rcplicas, a classical trajectory is integrated. Each replica trajcttory is monitored for a transition event by perfomling a quench after each 6Tb1o<:k of integration lime. When one processor (i) detects an event, all processors are notified to stop. The simulation clock is incremented by the sum of the trajectory times accumulated by all 7 replicas since the beginning. On the processor that identified the transition state replica (i) is integrated forward for a prechosen time during which new transit ions may occur. Replica (i) becomes the new configuration of the system and the sequence is repeated. Figure I : Snapsoots ofPRM D runs at 1700K Figure I repons some snapshots from the parallel replica simulation at T= 1700 K. Of the four rcplicas shown, three leads to ring closure. This reaction has been already studicd by Frenklaeh and co-workcrs who identified some possible reaction mechanisms U4} . The result using the current method gives us new infomlation that~ include the possibility of also forming substituted phenalene compounds. With this in mind, the transition events identified during the MD runs have been then analyzed using quantum chemical methods. The geometries of the reactants, products and transition states have been optimized using the AM I semiempirieal quantum method. Vibrational frequencies calculated at the same level have becn used for characterization of stationary points and zero-point enery (ZPE) corrections. All the energies quoted and discussed in the present paper include the ZPE correction. In order to obtain more reliable values for the energies, we have also carried out single-point calculations at the B3L YP level of theory (i.e. Becke' s three-parameter non local cxchange functional) with the non local correlation function of Lee, Yang and Parr), with the 6-3 IG(d,p) basis set [15. 16.17]. All quantum calcul ations werc done by using the G,lUssian 98 program [I 8]-A potentinl energy diagram for this reaction system along with the identification of species nomenclature is reponed in Fig.2. T51 %x \ , .. .. - ~ --. "H-I H+xgx M Figure 2: Relative energics diagram (S POlLYl' + ZPEAM1 ) (kcal/mol) for the reaction of acetylene with 4· phenanthryl. The reaction begins with the fomlation of an adduct, 4..::thynyl phenanthrene (AJ~HV through a first transition state (TS I) that lies only 5 kcallmol higher in energy than the reactants. A second transition state leads to the rotation of the CI-I=CH group that finnlly through TS3 fomlS ~H-l , that denotes radical fomled by addition of H to pyrene with the unpaired electron located at position I. The reaction for the cyclization becomes f\~H2 = ~H. I this pathway is in agreement with the results obtained by Wang and Frenklach [19]. From A.; H·I the system can then cyelize to fonn pyrene (A4) through the loss of H atom (dashed line) or through further rearrangcments to produce phcnalcne substituted 3 compound (PI). Figure 3 reports the optimized geometries for A4H· ] and PI computed at Ami level of theory. Inspection of the computed potential energy surfaces in Fig. 2 indicates that the reaction pathways for the fonnat ion of P I expericnces repulsion due 10 the sterically hindered aromatic bay. The presence of the repulsion implies elose proximity of the chemisorbcd CH=CH* radical group to the aromatic hydrogen. The transition state for the fonnation of P I lays 20 kcallmol below the reactants. Thc energy plot shows that both the pathways are possible in high temperature environment. Figure 3: Geomctries (bond lengths in angstroms, bond angles in degrees) of A4H·l and phen_sub optimized at AM I leveloftheOly. Detailed kinetic modeling studies have shown that the high.tcmpcrature gas· phase fonnatioll of PAH involves many highly reversible reaction steps. TIlese tightly balanced reaction steps playa particular important role in PAH fonnation and growth [20·22]. Their rates and their directions arc detemlincd 10 a largc dcgrce by thc corresponding equilibrium constants. It has been shown by Frenklach and Wamatz (23) thaI uncertainties in the thennochemical data can affect significantly PAH concentration profiles. The accuracy of thennodynamic data of PAH molecules and radicals which in tum detennincs the accuracy of the equilibrium constants, becomes critical for developing detailed kinetic models. Therefore, besidcs the analysis of reaction pathways, the Ihemlodynamic propertics of the key compounds have been calculatcd. Relative resul ts of semi..::mpirical techniques were shown to be consistent compared to molecular mechanics and therefore the viability of group corrected semi..::mpirieal techniques as developed by Wang and Frcnklach [23] was supported. This last techniques has been used in this paper to corrcct thc thcmlOdynamic data obtaincd through AMI calculations. The thennodynamic propCl1ies arc summarized in Table 1. Table I: Thermodynamic data of species considered in the present work (units: i'1Hr, kcaVmol; S, Cp cal/mol K) -,----..... ,-----,--,-,--...... ~----------i'1Hf 119.02 63.05 53.75 121.63 SfO 107.5 101.7 97.3 110.7 Cp,]OOK 52.5 47.5 44.5 52.1 Cp,500K 81.9 78.6 74.3 81.6 Cp,700K 101.5 99.5 94.7 lOlA Cp.900K 114.7 113.5 108.5 114.7 Cp,11l00K 119.7 118.8 113.7 119.8 Cp,1200K 127.6 127.1 121.8 127.7 Cp.1500K 135.8 135.5 130 135.9 """""'_~_,v..,,,,, -,,----~ Conclusions Molecular dynamics method was used to study the six-member ring cyclization reaction pathWtlys in combustion conditions. The reaction pathways analyzed in this paper are represented by the addition of acetylene to 4- phenanthryl radical and the ring cyc1ization to form pyrcne. This paper presents qualitatively results and shows the importance of Molecular Dynamics to evaluate reaction pathways, especially in combustion conditions. The Parallel Replica method for accelerating Molecular Dynamics calculations is used to screen reaction pathways. The infOiTIlation obtained through the use of Molecular Dynamics run are then analyzed with quantum chemical methods and them10dynamic data for the key compounds. Work is now underway on quantifying the kinetics of the possible reaction pathways for both the zig-zag and armchair surfaces, and reactions involving H migration. We will present these results along with further details about the methods used in a forthcoming publication. Acknowledgements This research is funded by the University of Utah Center for the Simulation of Accidental Fires and Explosions (GSAFE), funded by the Department of Encrgy, Lawrence Livennore National LaboratOlY, under subcontract B341493. The calculations presented in this paper were calTied out at the Utah Center for High Performance Computing, University of Utah that is acknowledged for computer time support. The authors thank Dr. A. 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Identification of pathways for polyaromatic growth using molecular dynamics

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Identification of pathways for polyaromatic growth using molecular dynamics

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