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Dynamical simulation of collision-induced dissociation of pyrene dimer cation

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Abstract

We report a theoretical investigation of the collision-induced dissociation of pyrene dimer cation, as recently investigated in the experimental work by Zamith et al. (J. Chem. Phys. 153, 054311 (2020)). Molecular dynamics simulations using potential energies and forces computed at the self-consistent charge density functional-based tight binding level were conducted for different collision energies between 2.5 and 30 eV. It appears that most of the dissociation occurs on a short timescale (less than 3 ps). The dynamical simulations allow to visualize the dissociation processes. At low collision energies, the dissociation cross section increases with collision energies, whereas it remains almost constant for collision energies greater than 10-15 eV. The analysis of the kinetic energy partition is used to get insights into the collision/dissociation processes at the atomic scale. The simulated time-of-flight mass spectra of parent and dissociation products are obtained from the combination of molecular dynamics simulations and phase space theory to address the short and long timescales dissociation, respectively. The agreement between the simulated and measured mass spectra suggests that the main processes are captured by this approach.

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References

  1. Eaves NA, Dworkin SB, Thomson MJ (2015) The importance of reversibility in modeling soot nucleation and condensation processes. Proc Comb Inst 35(2):1787

    Article  CAS  Google Scholar 

  2. Mao Q, van Duin ACT, Luo KH (2017) Formation of incipient soot particles from polycyclic aromatic hydrocarbons: a ReaxFF molecular dynamics study. Carbon 121:380

    Article  CAS  Google Scholar 

  3. Saggese C, Ferrario S, Camacho J, Cuoci A, Frassoldati A, Ranzi E, Wang H, Faravelli T (2015) Kinetic modeling of particle size distribution of soot in a premixed burner-stabilized stagnation ethylene flame. Combust Flame 162(9):3356

    Article  CAS  Google Scholar 

  4. Aubagnac-Karkar D, El Bakali A, Desgroux P (2018) Soot particles inception and PAH condensation modelling applied in a soot model utilizing a sectional method. Combust Flame 189:190

    Article  CAS  Google Scholar 

  5. Totton TS, Chakrabarti D, Misquitta AJ, Sander M, Wales DJ, Kraft M (2010) Modelling the internal structure of nascent soot particles. Combust Flame 157(5):909

    Article  CAS  Google Scholar 

  6. Chung SH, Violi A (2011) Peri-condensed aromatics with aliphatic chains as key intermediates for the nucleation of aromatic hydrocarbons. Proc Combust Inst 33(1):693

    Article  CAS  Google Scholar 

  7. Wang CS, Bartelt NC, Ragan R, Thürmer K (2018) Revealing the molecular structure of soot precursors. Carbon 129:537

    Article  CAS  Google Scholar 

  8. Sabbah H, Biennier L, Klippenstein SJ, Sims IR, Rowe BR (2010) Exploring the role of PAHs in the formation of soot: Pyrene dimerization. J Phys Chem Lett 1(19):2962

    Article  CAS  Google Scholar 

  9. Adkins EM, Giaccai JA, Miller JH (2017) Computed electronic structure of polynuclear aromatic hydrocarbon agglomerates. Proc Comb Inst 36(1):957

    Article  CAS  Google Scholar 

  10. Chakraborty D, Lischka H, Hase WL (2020) Dynamics of pyrene-dimer association and ensuing pyrene-dimer dissociation. J Phys Chem A 124(43):8907

    Article  CAS  PubMed  Google Scholar 

  11. Léger A, Puget JL (1984) Identification of the ’unidentified’ IR emission features of interstellar dust? Astron Astrophys 137:L5

    Google Scholar 

  12. Allamandola LJ, Tielens AGGM, Barker JR (1985) Polycyclic aromatic hydrocarbons and the unidentified infrared emission bands - auto exhaust along the milky way. Astrophys J Lett 290:L25

    Article  CAS  Google Scholar 

  13. Rapacioli M, Joblin C, Boissel P (2005) Spectroscopy of polycyclic aromatic hydrocarbons and very small grains in photodissociation regions. Astron Astrophys 429:193

    Article  CAS  Google Scholar 

  14. Berné O, Joblin C, Deville Y, Smith JD, Rapacioli M, Bernard JP, Thomas J, Reach W, Abergel A (2007) Analysis of the emission of very small dust particles from Spitzer spectro-imagery data using blind signal separation methods. Astron Astrophys 469:575

    Article  Google Scholar 

  15. Berné O, Joblin C, Rapacioli M, Thomas J, Cuillandre JC, Deville Y (2008) Extended red emission and the evolution of carbonaceous nanograins in NGC 7023. Astron Astrophys 479:L41

    Article  Google Scholar 

  16. Lei L, Yao Y, Zhang J, Tronrud D, Kong W, Zhang C, Xue L, Dontot L, Rapacioli M (2020) Electron diffraction of pyrene nanoclusters embedded in superfluid helium droplets. J Phys Chem Lett 11(3):724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Goulart M, Kuhn M, Rasul B, Postler J, Gatchell M, Zettergren H, Scheier P, Echt O (2017) The structure of coronene cluster ions inferred from H2 uptake in the gas phase. Phys Chem Chem Phys 19:27968

    Article  CAS  PubMed  Google Scholar 

  18. Birer Ö, Yurtsever E (2015) Dimer formation of perylene: an ultracold spectroscopic and computational study. J Mol Struct 1097:29

    Article  CAS  Google Scholar 

  19. Beitz T, Laudien R, Löhmannsröben HG, Kallies B (2006) Ion mobility spectrometric investigation of aromatic cations in the gas phase. J Phys Chem A 110(10):3514

    Article  CAS  PubMed  Google Scholar 

  20. Joblin C, Dontot L, Garcia GA, Spiegelman F, Rapacioli M, Nahon L, Parneix P, Pino T, Bréchignac P (2017) Size effect in the ionization energy of PAH clusters. J Phys Chem Lett 8(15):3697

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Roser JE, Ricca A (2015) Polycyclic aromatic hydrocarbon clusters as sources of interstellar aromatic infrared emission. Astrophys J 801(2):108

    Article  Google Scholar 

  22. Lemmens AK, Gruet S, Steber AL, Antony J, Grimme S, Schnell M, Rijs AM (2019) Far-IR and UV spectral signatures of controlled complexation and microhydration of the polycyclic aromatic hydrocarbon acenaphthene. Phys Chem Chem Phys 21:3414

    Article  CAS  PubMed  Google Scholar 

  23. Fioressi SE, Binning RC, Bacelo DE (2008) Effects of cluster formation on spectra of benzopyrene and benzopyrene. Chem Phys Lett 454(4):269

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Friha H, Féraud G, Pino T, Parneix P, Dhaouadi Z, Bréchignac P (2012) Electronic spectra of cationic PAH and PAH clusters. EAS Publ Ser 58:373

    Article  Google Scholar 

  25. Schmidt M, Masson A, Bréchignac C (2006) Coronene cluster experiments: stability and thermodynamics. Int J Mass Spectrom 252(2):173

    Article  CAS  Google Scholar 

  26. Gatchell M, Stockett MH, de Ruette N, Chen T, Giacomozzi L, Nascimento RF, Wolf M, Anderson EK, Delaunay R, Vizcaino V, Rousseau P, Adoui L, Huber BA, Schmidt HT, Zettergren H, Cederquist H (2015) Failure of hydrogenation in protecting polycyclic aromatic hydrocarbons from fragmentation. Phys Rev A 92:050702

    Article  Google Scholar 

  27. Holm AIS, Zettergren H, Gatchell M, Johansson HAB, Seitz F, Schmidt HT, Rousseau P, Ławicki A, Capron M, Domaracka A, Lattouf E, Maclot S, Maisonny R, Chesnel JY, Manil B, Adoui L, Huber BA, Cederquist H (2012) Ionization and fragmentation of cold clusters of PAH molecules -collisions with keV ions. J Phys Conf Ser 388(1):012051

    Article  Google Scholar 

  28. Johansson HAB, Zettergren H, Holm AIS, Seitz F, Schmidt HT, Rousseau P, Ławicki A, Capron M, Domaracka A, Lattouf E, Maclot S, Maisonny R, Manil B, Chesnel JY, Adoui L, Huber BA, Cederquist H (2011) Ionization and fragmentation of polycyclic aromatic hydrocarbon clusters in collisions with keV ions. Phys Rev A 84(4):043201

    Article  Google Scholar 

  29. Holm AIS, Zettergren H, Johansson HAB, Seitz F, Rosén S, Schmidt HT, Ławicki A, Rangama J, Rousseau P, Capron M, Maisonny R, Adoui L, Méry A, Manil B, Huber BA, Cederquist H (2010) Ions colliding with cold polycyclic aromatic hydrocarbon clusters. Phys Rev Lett 105(21):213401

    Article  CAS  PubMed  Google Scholar 

  30. Gatchell M, Rousseau P, Domaracka A, Stockett MH, Chen T, Schmidt HT, Chesnel JY, Méry A, Maclot S, Adoui L, Huber BA, Zettergren H, Cederquist H (2014) Ions colliding with mixed clusters of \({\rm C}_{60}\) and coronene: fragmentation and bond formation. Phys Rev A 90:022713

    Article  Google Scholar 

  31. Delaunay R, Gatchell M, Rousseau P, Domaracka A, Maclot S, Wang Y, Stockett MH, Chen T, Adoui L, Alcamí M, Martín F, Zettergren H, Cederquist H, Huber BA (2015) Molecular growth inside of polycyclic aromatic hydrocarbon clusters induced by ion collisions. J Phys Chem Lett 6(9):1536

    Article  CAS  PubMed  Google Scholar 

  32. Zamith S, Ji MC, L’Hermite JM, Joblin C, Dontot L, Rapacioli M, Spiegelman F (2019) Thermal evaporation of pyrene clusters. J Chem Phys 151(19):194303

    Article  PubMed  Google Scholar 

  33. Gámez F, Hortal AR, Martínez-Haya B, Soltwisch J, Dreisewerd K (2014) Ultraviolet laser desorption/ionization mass spectrometry of single-core and multi-core polyaromatic hydrocarbons under variable conditions of collisional cooling: insights into the generation of molecular ions, fragments and oligomers. J Mass Spectrom 49(11):1127

    Article  PubMed  Google Scholar 

  34. Zhen J, Chen T, Tielens AGGM (2018) Laboratory photochemistry of pyrene clusters: an efficient way to form large PAHs. Astrophys J 863(2):128

    Article  Google Scholar 

  35. Bréchignac P, Schmidt M, Masson A, Pino T, Parneix P, Bréchignac C (2005) Photoinduced products from cold coronene clusters. Astron Astrophys 442(1):239

    Article  Google Scholar 

  36. Chen T (2018) Formation of covalently bonded polycyclic aromatic hydrocarbons in the interstellar medium. Astrophys J 866(2):113

    Article  Google Scholar 

  37. Yurtsever E (2010) Stacking of triphenylene: characterization of the potential energy surface. Theo Chem Acc 127(3):133–139

    Article  CAS  Google Scholar 

  38. Piacenza M, Grimme S (2005) Van der Waals complexes of polar aromatic molecules: unexpected structures for dimers of azulene. J Am Chem Soc 127(42):14841

    Article  CAS  PubMed  Google Scholar 

  39. Podeszwa R (2010) Interactions of graphene sheets deduced from properties of polycyclic aromatic hydrocarbons. J Chem Phys 132:044704

    Article  PubMed  Google Scholar 

  40. Zhao Y, Truhlar DG (2008) A prototype for graphene material simulation; structures and interaction potentials of coronene dimers. J Phys Chem C 112:4061

    Article  CAS  Google Scholar 

  41. Sancho-García JC, Pérez-Jiménez AJ (2009) Charge-transport properties of prototype molecular materials for organic electronics based on graphene nanoribbons. Phys Chem Chem Phys 11:2741

    Article  PubMed  Google Scholar 

  42. Rapacioli M, Spiegelman F, Talbi D, Mineva T, Goursot A, Heine T, Seifert G (2009) Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters. J Chem Phys 130:244304

    Article  PubMed  Google Scholar 

  43. Obolensky OI, Semenikhina VV, Solov’yov AV, Greiner W (2007) Interplay of electrostatic and van der Waals forces in coronene dimer. Int J Quant Chem 107(6):1335

    Article  CAS  Google Scholar 

  44. Bartolomei M, Pirani F, Marques JMC (2017) Modeling coronene nanostructures: analytical potential, stable configurations and Ab initio energies. J Phys Chem C 121(26):14330

    Article  CAS  Google Scholar 

  45. Ricca A, Charles J, Bauschlicher W, Allamandola LJ (2013) The infrared spectroscopy of neutral polycyclic aromatic hydrocarbon clusters. Astrophys J 776(1):31

    Article  Google Scholar 

  46. Piuzzi F, Dimicoli I, Mons M, Millié P, Brenner V, Zhao Q, Soep B, Tramer A (2002) Spectroscopy, dynamics and structures of jet formed anthracene clusters. Chem Phys 275(1):123

    Article  CAS  Google Scholar 

  47. Totton TS, Misquitta AJ, Kraft M (2011) A transferable electrostatic model for intermolecular interactions between polycyclic aromatic hydrocarbons. Chem Phys Lett 510(1):154

    Article  CAS  Google Scholar 

  48. Grančič P, Bylsma R, Meekes H, Cuppen HM (2015) Evaluation of all-atom force fields for anthracene crystal growth. Cryst Growth Des 15(4):1625

    Article  Google Scholar 

  49. Herdman JD, Miller JH (2008) Intermolecular potential calculations for polynuclear aromatic hydrocarbon clusters. J Phys Chem A 112(28):6249

    Article  CAS  PubMed  Google Scholar 

  50. Easter DC, Roof JA, Butts LJ (2007) A Monte Carlo study of isomers and structural evolution in benzene-cyclohexane clusters: (C6H6)(C6H12)n, n = 3–7, 12. J Phys Chem A 111(50):12914

    Article  CAS  PubMed  Google Scholar 

  51. Totton TS, Misquitta AJ, Kraft M (2012) A quantitative study of the clustering of polycyclic aromatic hydrocarbons at high temperatures. Phys Chem Chem Phys 14:4081

    Article  CAS  PubMed  Google Scholar 

  52. Bowal K, Martin JW, Kraft M (2019) Partitioning of polycyclic aromatic hydrocarbons in heterogeneous clusters. Carbon 143:247

    Article  CAS  Google Scholar 

  53. Pascazio L, Sirignano M, D’Anna A (2017) Simulating the morphology of clusters of polycyclic aromatic hydrocarbons: the influence of the intermolecular potential. Combust Flame 185:53

    Article  CAS  Google Scholar 

  54. Chen D, Totton TS, Akroyd JWJ, Mosbach S, Kraft M (2014) Size-dependent melting of polycyclic aromatic hydrocarbon nano-clusters: a molecular dynamics study. Carbon 67:79

    Article  CAS  Google Scholar 

  55. Nakamura M, Ichimura A (2013) Stability of multiply charged clusters of polycyclic aromatic hydrocarbons. Physica Scripta 2013(T156):014063

    Article  Google Scholar 

  56. Takeuchi H (2013) Structures, stability, and growth sequence patterns of small homoclusters of naphthalene, anthracene, phenanthrene, phenalene, naphthacene, and pyrene. Comput Theor Chem 1021:84

    Article  CAS  Google Scholar 

  57. Calvo F, Yurtsever E, Birer Ö (2016) Possible formation of metastable PAH dimers upon pickup by helium droplets. J Phys Chem A 120(10):1727

    Article  CAS  PubMed  Google Scholar 

  58. Gräfenstein J, Cremer D (2009) The self-interaction error and the description of non-dynamic electron correlation in density functional theory, Theo. Chem Acc : Theo Comp Model 123:171

    Article  Google Scholar 

  59. Dontot L, Spiegelman F, Rapacioli M (2019) Structures and energetics of neutral and cationic pyrene clusters. J Phys Chem A 123(44):9531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Dontot L, Suaud N, Rapacioli M, Spiegelman F (2016) An extended DFTB-CI model for charge-transfer excited states in cationic molecular clusters: model studies versus ab initio calculations in small PAH clusters. Phys Chem Chem Phys 18:3545

    Article  CAS  PubMed  Google Scholar 

  61. Dontot L, Spiegelman F, Zamith S, Rapacioli M (2020) Dependence upon charge of the vibrational spectra of small polycyclic aromatic hydrocarbon clusters: the example of pyrene. Eur Phys J D 74(11):1

    Article  Google Scholar 

  62. Porezag D, Frauenheim T, Köhler T, Seifert G, Kaschner R (1995) Construction of tight-binding-like potentials on the basis of density-functional theory: application to carbon. Phys Rev B 51:12947

    Article  CAS  Google Scholar 

  63. Seifert G, Porezag D, Frauenheim T (1996) Calculations of molecules, clusters, and solids with a simplified LCAO-DFT-LDA scheme Int. J Quantum Chem 58:185

    Article  CAS  Google Scholar 

  64. Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys Rev B 58:7260

    Article  CAS  Google Scholar 

  65. Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M (2020) Density-functional tight-binding: basic concepts and applications to molecules and clusters. Adv Phys X 5(1):1710252

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Rapacioli M, Spiegelman F, Scemama A, Mirtschink A (2011) Modeling charge resonance in cationic molecular clusters: combining DFT-tight binding with configuration interaction. J Chem Theor Comput 7:44

    Article  CAS  Google Scholar 

  67. Gatchell M, Zettergren H, Cederquist H, Schmidt H (2016) Molecular hole punching : Impulse driven reactions in molecules and molecular clusters. Ph.D. thesis, Stockholm University, Stockholm

  68. Gatchell M, Zettergren H (2016) Knockout driven reactions in complex molecules and their clusters. J Phys B 49(16):162001

    Article  Google Scholar 

  69. Zamith S, L’Hermite JM, Dontot L, Zheng L, Rapacioli M, Spiegelman F, Joblin C (2020) Threshold collision induced dissociation of pyrene cluster cations. J Chem Phys 153:054311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Elstner M, Seifert G (2014) Density functional tight binding. Philos Trans R Soc A 372(2011):20120483

    Article  Google Scholar 

  71. Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M (2020) Density-functional tight-binding: basic concepts and applications to molecules and clusters. Adv Phys-X 5(1):1710252

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Iftner C, Simon A, Korchagina K, Rapacioli M, Spiegelman F (2014) A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: application to (C6H6)+/0Arn clusters. J Chem Phys 140(3):034301

    Article  PubMed  Google Scholar 

  73. Frenzel J, Oliveira AF, Jardillier N, Heine T, Seifert G, Semi-relativistic, self-consistent charge Slater-Koster tables for density-functional based tight-binding (DFTB) for materials science simulations (TU Dresden, 2004-2009)

  74. Li J, Zhu T, Cramer C, Truhlar D (1998) New class IV charge model for extracting accurate partial charges from wave functions. J Phys Chem A 102:1820

    Article  CAS  Google Scholar 

  75. Kukk E, Ha D, Wang Y, Piekarski DG, Diaz-Tendero S, Kooser K, Itälä E, Levola H, Alcamí M, Rachlew E et al (2015) Internal energy dependence in X-ray-induced molecular fragmentation: an experimental and theoretical study of thiophene. Phys Rev A 91(4):043417

    Article  Google Scholar 

  76. Simon A, Rapacioli M, Rouaut G, Trinquier G, Gadéa F (2017) Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies. Philos Trans R Soc A 375(2092):20160195

    Article  Google Scholar 

  77. Simon A, Champeaux JP, Rapacioli M, Moretto-Capelle P, Gadéa X, Florent Sence M (2018) Dissociation of polycyclic aromatic hydrocarbons at high energ: MD/DFTB simulations versus collision experiments. Theor Chem Acc 137(7):106

    Article  Google Scholar 

  78. Rapacioli M, Cazaux S, Foley N, Simon A, Hoekstra R, Schlathölter T (2018) Atomic hydrogen interactions with gas-phase coronene cations: hydrogenation versus fragmentation. Phys Chem Chem Phys 20(35):22427

    Article  CAS  PubMed  Google Scholar 

  79. Nosé S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 81(1):511

    Article  Google Scholar 

  80. Hoover WG (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev A 31(3):1695

    Article  CAS  Google Scholar 

  81. Heine T, Rapacioli M, Patchkovskii S, Frenzel J, Koster A,Calaminici P, Duarte H, Escalante S, Flores-Moreno R, Goursot A(2009) demonnano

  82. Braud I, Zamith S, L’Hermite JM (2017) A gas aggregation source for the production of heterogeneous molecular clusters. Rev Sci Instrum 88(4):043102

    Article  CAS  PubMed  Google Scholar 

  83. Chirot F, Zamith S, Labastie P, L’Hermite JM (2006) New device to study unimolecular cluster nucleation. Rev Sci Instrum 77(6):063108

    Article  Google Scholar 

  84. Levine D, Bernstein RB (1987) Molecular reaction dynamics and chemical reactivity. Oxford University Press, Oxford

    Google Scholar 

  85. Chen T, Gatchell M, Stockett MH, Alexander JD, Zhang Y, Rousseau P, Domaracka A, Maclot S, Delaunay R, Adoui L et al (2014) Absolute fragmentation cross sections in atom-molecule collisions: scaling laws for non-statistical fragmentation of polycyclic aromatic hydrocarbon molecules. J Chem Phys 140(22):224306

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors acknowledge the supercomputing facility of CALMIP for generous allocation of computer resources. The authors declare that there has been no significant financial support for this work.

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Zheng, L., Zamith, S. & Rapacioli, M. Dynamical simulation of collision-induced dissociation of pyrene dimer cation. Theor Chem Acc 140, 19 (2021). https://doi.org/10.1007/s00214-020-02716-7

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