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Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

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Abstract

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

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References

  1. D. Schardt, T. Elsässer, D. Schulz-Ertner, Rev. Mod. Phys. 82, 383 (2010)

    Article  ADS  Google Scholar 

  2. E. Surdutovich, A.V. Solov’yov, Eur. Phys. J. D 66, 206 (2012)

    Article  ADS  Google Scholar 

  3. A.G.G.M. Tielens, Rev. Mod. Phys. 85, 1021 (2013)

    Article  ADS  Google Scholar 

  4. Astrobiology: The Quest for the Conditions of Life, edited by G. Horneck, C. Baumstark-Khan (Springer-Verlag Berlin Heidelberg, 2002)

  5. M. Huth, F. Porrati, C. Schwalb, M. Winhold, R. Sachser, M. Dukic, J. Adams, G. Fantner, Beilstein J. Nanotechnol. 3, 597 (2012)

    Article  Google Scholar 

  6. I. Utke, P. Hoffmann, J. Melngailis, J. Vac. Sci. Technol. B 26, 1197 (2008)

    Article  Google Scholar 

  7. B. Wu, A. Kumar, J. Vac. Sci. Technol. B 25, 1743 (2007)

    Article  Google Scholar 

  8. A.M. Hawryluk, L.G. Seppala, J. Vac. Sci. Technol. B 6, 2162 (1988)

    Article  Google Scholar 

  9. F. Heidet, N.R. Brown, M. Haj Tahar, Rev. Accelerat. Sci. Technol. 8, 99 (2015)

    Article  ADS  Google Scholar 

  10. P. Dinh, P.G. Reinhard, E. Suraud, Phys. Rep. 485, 43 (2010)

    Article  ADS  Google Scholar 

  11. J. Maruhn, P. Reinhard, E. Suraud, Simple Models of Many-Fermion Systems (Springer-Verlag, Berlin, Heidelberg, 2010)

  12. D. Jacquemin, V. Wathelet, E.A. Perpéte, C. Adamo, J. Chem. Theory Comput. 5, 2420 (2009)

    Article  Google Scholar 

  13. A.D. Bochevarov, E. Harder, T.F. Hughes, J.R. Greenwood, D.A. Braden, D.M. Philipp, D. Rinaldo, M.D. Halls, J. Zhang, R.A. Friesner, Int. J. Quantum Chem. 113, 2110 (2013)

    Article  Google Scholar 

  14. K. Sanbonmatsu, C.S. Tung, J. Struct. Biol. 157, 470 (2007)

    Article  Google Scholar 

  15. G. Zhao, J.R. Perilla, E.L. Yufenyuy, X. Meng, B. Chen, J. Ning, J. Ahn, A.M. Gronenborn, K. Schulten, C. Aiken, P. Zhang, Nature 497, 643 (2013)

    Article  ADS  Google Scholar 

  16. P. Husen, I.A. Solov’yov, J. Am. Chem. Soc. 138, 12150 (2016)

    Article  Google Scholar 

  17. A.C. Pan, T.M. Weinreich, S. Piana, D.E. Shaw, J. Chem. Theory Comput. 12, 1360 (2016)

    Article  Google Scholar 

  18. R. Salomon-Ferrer, A.W. Gotz, D. Poole, S. Le Grand, R.C. Walker, J. Chem. Theory Comput. 9, 3878 (2013)

    Article  Google Scholar 

  19. A.K. Rappé, C.J. Casewit, Molecular Mechanics Across Chemistry (University Science Books, 1997)

  20. J. Gumbart, E. Schreiner, D.N. Wilson, R. Beckmann, K. Schulten, Biophys. J. 103, 331 (2012)

    Article  ADS  Google Scholar 

  21. J. Shim, G.I. Humphreys, B.M. Venkatesan, J.M. Munz, X. Zou, C. Sathe, K. Schulten, F. Kosari, A.M. Nardulli, G. Vasmatzis, R. Bashir, Sci. Rep. 3, 1389 (2013)

    ADS  Google Scholar 

  22. E. Sjulstok, J.M.H. Olsen, I.A. Solov’yov, Sci. Rep. 5, 18446 (2015)

    Article  ADS  Google Scholar 

  23. G. Lüdemann, I.A. Solov’yov, T. Kubař, M. Elstner, J. Am. Chem. Soc. 137, 1147 (2015)

    Article  Google Scholar 

  24. B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, M. Karplus, J. Comput. Chem. 4, 187 (1983)

    Article  Google Scholar 

  25. D.A. Case, T.E. Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, A. Onufriev, C. Simmerling, B. Wang, R.J. Woods, J. Comput. Chem. 26, 1668 (2005)

    Article  Google Scholar 

  26. D.V.D. Spoel, E. Lindahl, B. Hess, G. Groenhof, A. Mark, H. Berendsen, J. Comput. Chem. 26, 1701 (2005)

    Article  Google Scholar 

  27. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, K. Schulten, J. Comput. Chem. 26, 1781 (2005)

    Article  Google Scholar 

  28. I.A. Solov’yov, A.V. Yakubovich, P.V. Nikolaev, I. Volkovets, A.V. Solov’yov, J. Comput. Chem. 33, 2412 (2012)

    Article  Google Scholar 

  29. G.B. Sushko, I.A. Solov’yov, A.V. Verkhovtsev, S.N. Volkov, A.V. Solov’yov, Eur. Phys. J. D 70, 12 (2016)

    Article  ADS  Google Scholar 

  30. I.A. Solov’yov, G.B. Sushko, A.V. Verkhovtsev, A.V. Korol, A.V. Solov’yov, MBN Explorer: Dynamics of Biomolecular Systems and Self-organization (Polytechnic University Publishing House, St. Petersburg State Polytechnic University, St. Petersburg, Russia, 2015)

  31. I.A. Solov’yov, G.B. Sushko, A.V. Verkhovtsev, A.V. Korol, A.V. Solov’yov, MBN Explorer: Simulations of Nanomaterials Structure and Dynamics (Polytechnic University Publishing House, St. Petersburg State Polytechnic University, St. Petersburg, Russia, 2015)

  32. V.V. Dick, I.A. Solov’yov, A.V. Solov’yov, Phys. Rev. B 84, 115408 (2011)

    Article  ADS  Google Scholar 

  33. V.V. Dick, I.A. Solov’yov, A.V. Solov’yov, J. Phys.: Conf. Ser. 248, 012025 (2010)

    ADS  Google Scholar 

  34. M. Panshenskov, I.A. Solov’yov, A.V. Solov’yov, J. Comput. Chem. 35, 1317 (2014)

    Article  Google Scholar 

  35. I.A. Solov’yov, A.V. Solov’yov, N. Kébaili, A. Masson, C. Bréchignac, Phys. Stat. Sol. B 251, 609 (2014)

    Article  ADS  Google Scholar 

  36. I.A. Solov’yov, A.V. Solov’yov, J. Phys.: Conf. Ser. 438, 012006 (2013)

    ADS  Google Scholar 

  37. G.B. Sushko, V.G. Bezchastnov, I.A. Solov’yov, A.V. Korol, W. Greiner, A.V. Solov’yov, J. Comput. Phys. 252, 404 (2013)

    Article  ADS  Google Scholar 

  38. G. Sushko, A. Korol, W. Greiner, A. Solov’yov, J. Phys.: Conf. Ser. 438, 012018 (2013)

    ADS  Google Scholar 

  39. G. Sushko, V. Bezchastnov, A. Korol, W. Greiner, A. Solov’yov, R. Polozkov, V. Ivanov, J. Phys.: Conf. Ser. 438, 012019 (2013)

    ADS  Google Scholar 

  40. G.B. Sushko, A.V. Korol, A.V. Solov’yov, Nucl. Instrum. Meth. Phys. Res. B 355, 39 (2015)

    Article  ADS  Google Scholar 

  41. A.V. Verkhovtsev, S. Schramm, A.V. Solov’yov, Eur. Phys. J. D 68, 246 (2014)

    Article  ADS  Google Scholar 

  42. A.V. Verkhovtsev, M. Hanauske, A.V. Yakubovich, A.V. Solov’yov, Comput. Mater. Sci. 76, 80 (2013)

    Article  Google Scholar 

  43. G.B. Sushko, A.V. Verkhovtsev, A.V. Solov’yov, J. Phys. Chem. A 118, 8426 (2014)

    Article  Google Scholar 

  44. I.A. Solov’yov, M. Mathew, A.V. Solov’yov, W. Greiner, Phys. Rev. E 78, 051601 (2008)

    Article  ADS  Google Scholar 

  45. J. Geng, I.A. Solov’yov, D.G. Reid, P. Skelton, A.E.H. Wheatley, A.V. Solov’yov, B.F.G. Johnson, Phys. Rev. B 81, 214114 (2010)

    Article  ADS  Google Scholar 

  46. J. Geng, I.A. Solov’yov, W. Zhou, A.V. Solov’yov, B.F.G. Johnson, J. Phys. Chem. C 113, 6390 (2009)

    Article  Google Scholar 

  47. I.A. Solov’yov, J. Geng, A.V. Solov’yov, B.F. Johnson, Chem. Phys. Lett. 472, 166 (2009)

    Article  ADS  Google Scholar 

  48. P. Moskovkin, M. Panshenskov, S. Lucas, A.V. Solov’yov, Phys. Stat. Sol. B 251, 1456 (2014)

    Article  ADS  Google Scholar 

  49. G.B. Sushko, A.V. Verkhovtsev, A.V. Yakubovich, S. Schramm, A.V. Solov’yov, J. Phys. Chem. A 118, 6685 (2014)

    Article  Google Scholar 

  50. A.V. Verkhovtsev, A.V. Yakubovich, G.B. Sushko, M. Hanauske, A.V. Solov’yov, Comput. Mater. Sci. 76, 20 (2013)

    Article  Google Scholar 

  51. A.V. Yakubovich, E. Surdutovich, A.V. Solov’yov, J. Phys.: Conf. Ser. 373, 012014 (2012)

    ADS  Google Scholar 

  52. E. Surdutovich, A.V. Yakubovich, A.V. Solov’yov, Eur. Phys. J. D 60, 101 (2010)

    Article  ADS  Google Scholar 

  53. E. Surdutovich, A.V. Yakubovich, A.V. Solov’yov, Sci. Rep. 3, 1289 (2013)

    Article  ADS  Google Scholar 

  54. E. Surdutovich, A.V. Solov’yov, Eur. Phys. J. D 68, 353 (2014)

    Article  ADS  Google Scholar 

  55. K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A.D. Mackerell Jr., J. Comput. Chem. 31, 671 (2010)

    Google Scholar 

  56. R.B. Best, X. Zhu, J. Shim, P.E.M. Lopes, J. Mittal, M. Feig, A.D. MacKerell, J. Chem. Theory Comput. 8, 3257 (2012)

    Article  Google Scholar 

  57. A.D. MacKerell, Jr., et al., J. Phys. Chem. B 102, 3586 (1998)

    Article  Google Scholar 

  58. J.D. Fowlkes, P.D. Rack, ACS nano 4, 1619 (2010)

    Article  Google Scholar 

  59. A.M. Barragan, A.R. Crofts, K. Schulten, I.A. Solov’yov, J. Phys. Chem. B 119, 433 (2015)

    Article  Google Scholar 

  60. E. Fermi, J. Pasta, S. Ulam, Studies of nonlinear problems (Los Alamos report LA-1940, 1955)

  61. N. Silvis-Cividjian, C. Hagen, L. Leunissen, P. Kruit, Microelectron. Eng. 61, 693 (2002)

    Article  Google Scholar 

  62. F. Salvat-Pujol, H.O. Jeschke, R. Valentí, Beilstein J. Nanotechnol. 4, 781 (2013)

    Article  Google Scholar 

  63. G. Cetini, O. Gambino, Accad. Sci. Torino., Classe Sci. Fis. Mat. Nat. 97, 1197 (1963)

    Google Scholar 

  64. K. Muthukumar, I. Opahle, J. Shen, H.O. Jeschke, R. Valentí, Phys. Rev. B 84, 205442 (2011)

    Article  ADS  Google Scholar 

  65. A.V. Yakubovich, A.V. Verkhovtsev, M. Hanauske, A.V. Solov’yov, Comput. Mater. Sci. 76, 60 (2013)

    Article  Google Scholar 

  66. M. Huth, D. Klingenberger, C. Grimm, F. Porrati, R. Sachser, N. J. Phys. 11, 033032 (2009)

    Article  Google Scholar 

  67. M. Finnis, J. Sinclair, Philos. Mag. A 50, 45 (1984)

    Article  ADS  Google Scholar 

  68. A.P. Sutton, J. Chen, Philos. Mag. Lett. 61, 139 (1990)

    Article  ADS  Google Scholar 

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Author information

Authors and Affiliations

  1. MBN Research Center, Altenhöferallee 3, 60438, Frankfurt am Main, Germany

    Gennady B. Sushko & Andrey V. Solov’yov

  2. University of Southern Denmark (SDU), Campusvej 55, 5230, Odense M, Denmark

    Ilia A. Solov’yov

Authors
  1. Gennady B. Sushko
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  2. Ilia A. Solov’yov
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  3. Andrey V. Solov’yov
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Correspondence to Ilia A. Solov’yov.

Additional information

Contribution to the Topical Issue “Atomic Cluster Collisions (7th International Symposium)”, edited by Gerardo Delgado Barrio, Andrey Solov’yov, Pablo Villarreal, Rita Prosmiti.

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Sushko, G., Solov’yov, I. & Solov’yov, A. Molecular dynamics for irradiation driven chemistry: application to the FEBID process*. Eur. Phys. J. D 70, 217 (2016). https://doi.org/10.1140/epjd/e2016-70283-5

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