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First-principle-based MD description of azobenzene molecular rods

Abstract

Extensive density functional theory (DFT) calculations have been performed to develop a force field for the classical molecular dynamics (MD) simulations of various azobenzene derivatives. Besides azobenzene, we focused on a thiolated azobenzene’s molecular rod (4′-{[(1,1′-biphenyl)-4-yl]diazenyl}-(1,1′-biphenyl)-4-thiol) that has been previously demonstrated to photoisomerize from trans to cis with high yields on surfaces. The developed force field is an extension of OPLS All Atoms, and key bonding parameters are parameterized to reproduce the potential energy profiles calculated by DFT. For each of the parameterized molecule, we propose three sets of parameters: one best suited for the trans configuration, one for the cis configuration, and finally, a set able to describe both at a satisfactory degree. The quality of the derived parameters is evaluated by comparing with structural and vibrational experimental data. The developed force field opens the way to the classical MD simulations of self-assembled monolayers (SAMs) of azobenzene’s molecular rods, as well as to the quantum mechanics/molecular mechanics study of photoisomerization in SAMs.

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References

  1. Balzani V, Venturi M, Credi A (2004) Molecular devices and machines: a journey into the Nanoworld. Wiley, Weinheim

    Google Scholar 

  2. Browne WR, Feringa BL (2006) Nat Nanotechnol 1:25–35

    Article  CAS  Google Scholar 

  3. Badjic JD, Balzani V, Credi A, Silvi S, Stoddart JF (2004) Science 303:1845–1849

    Article  CAS  Google Scholar 

  4. Pace G, Ferri V, Grave C, Elbing M, Zharnikov M, Mayor M, Rampi MA, Samorì P (2007) Proc Natl Acad Sci USA 104:9937–9942

    Article  CAS  Google Scholar 

  5. Ferri V, Elbing M, Pace G, Dickey MD, Zharnikov M, Samorì P, Mayor M, Rampi MA (2008) Angew Chem Int Ed 47:3407–3409

    Article  CAS  Google Scholar 

  6. Bléger D, Yu Z, Hecht S (2011) Chem Commun 47:12260–12266

    Article  Google Scholar 

  7. Bléger D, Ciesielski A, Samorì P, Hecht S (2010) Chem Eur J 16:14256–14260

    Article  Google Scholar 

  8. Gahl C, Schmidt R, Brete D, McNellis ER, Freyer W, Carley R, Reuter K, Weinelt M (2010) J Am Chem Soc 132:1831–1838

    Article  CAS  Google Scholar 

  9. Mar W, Klein ML (1994) Langmuir 10:188–196

    Article  CAS  Google Scholar 

  10. Gannon G, Greer JC, Larsson JA, Thompson D (2010) ACS Nano 4:921–932

    Article  CAS  Google Scholar 

  11. Tirosh E, Benassi E, Pipolo S, Mayor M, Valášek M, Frydman V, Corni S, Cohen SR (2011) Beilstein J Nano 2:834–844

    Article  CAS  Google Scholar 

  12. Tiberio G, Muccioli L, Berardi R, Zannoni C (2010) ChemPhysChem 11:1018–1028

    Article  CAS  Google Scholar 

  13. Ciminelli C, Granucci G, Persico M (2008) Chem Phys 349:325–333

    Article  CAS  Google Scholar 

  14. Cusati T, Granucci G, Persico M (2011) J Am Chem Soc 133:5109–5123

    Article  CAS  Google Scholar 

  15. Böckmann M, Peter C, Delle Site L, Doltsinis NL, Kremer K, Marx D (2007) J Chem Theory Comput 3:1789–1802

    Article  Google Scholar 

  16. Böckmann M, Doltsinis NL, Marx D (2010) Angew Chem Int Ed 49:3382–3384

    Article  Google Scholar 

  17. Turanský R, Konôpka M, Doltsinis NL, Stich I, Marx D (2010) Phys Chem Chem Phys 12:13922–13932

    Article  Google Scholar 

  18. Böckmann M, Marx D, Peter C, Site LD, Kremer K, Doltsinis NL (2011) Phys Chem Chem Phys 13:7604–7621

    Article  Google Scholar 

  19. Schäfer LV, Müller EM, Gaub HE, Grubmüller H (2007) Angew Chem Int Ed 46:2232–2237

    Article  Google Scholar 

  20. Jorgensen WL, Tirado-Rivers J (1988) J Am Chem Soc 110:1657–1666

    Article  CAS  Google Scholar 

  21. Palmo K, Mannfors B, Mirkin N, Krimm S (2003) Biopolymers 68:383–394

    Article  CAS  Google Scholar 

  22. Maple J, Dinur U, Hagler A (1988) Proc Natl Acad Sci USA 85:5350–5354

    Article  CAS  Google Scholar 

  23. Dasgupta S, Yamasaki T, Goddard W III (1996) J Chem Phys 104:2898–2920

    Article  CAS  Google Scholar 

  24. Cacelli I, Prampolini G (2007) J Chem Theory Comput 3:1803–1817

    Article  CAS  Google Scholar 

  25. Cacelli I, Cimoli A, Lavotto PR, Prampolini G (2012) J Comput Chem 33:1055–1067

    Article  CAS  Google Scholar 

  26. Moré J (1978) The Levenberg-Marquardt algorithm: implementation and theory. In: Watson GA (ed) Numerical analysis, vol 630. Springer, Berlin, p 105

    Chapter  Google Scholar 

  27. Moré J, Wright S (1993) Optimization software guide, In: Frontiers in applied mathematics, Number 14, SIAM. (ISBN: 978-0-898713-22-0; Link to SIAM title listing); MINPACK-1, available from netlib. http://www.netlib.org/minpack

  28. Sinha P, Boesch SE, Gu C, Wheeler RA, Wilson AK (2004) J Phys Chem A 108:9213–9217

    Article  CAS  Google Scholar 

  29. Becke AD (1993) J Chem Phys 98:5648–5652

    Article  CAS  Google Scholar 

  30. Frisch MJ, Trucks GW, Schlegel HB et al (2009) Gaussian 09, Revision A.02, Inc., Wallingford

  31. Cieplak P, Cornell WD, Bayly C, Kollman PA (1995) J Comput Chem 16:1357–1377

    Article  CAS  Google Scholar 

  32. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) J Comput Chem 25:1157–1174

    Article  CAS  Google Scholar 

  33. Frenkel D, Smit B (2002) Understanding molecular simulations. Academic Press, San Diego

    Google Scholar 

  34. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) J Chem Theory Comput 4:435–447

    Article  CAS  Google Scholar 

  35. Wang L, Xu W, Yi C, Wang X (2009) J Mol Graph Mod 27:792–796

    Article  CAS  Google Scholar 

  36. Bouwstra JA, Schouten A, Kroon J (1983) Acta Crystallogr Sect C 39:1121–1123

    Article  Google Scholar 

  37. Traetterberg M, Hilmo I, Hagen K (1977) J Mol Struct 39:231–239

    Article  Google Scholar 

  38. Cembra A, Bernardi F, Garavelli M, Gagliardi L, Orlandi G (2004) J Am Chem Soc 126:3234–3243

    Article  Google Scholar 

  39. Wang L, Wang X (2007) J Mol Struct (Theochem) 847:1–9

    Article  CAS  Google Scholar 

  40. Wang L, Xu J, Zhou H, Yi C, Xu W (2009) J Photochem Photobiol A Chem 205:104–108

    Article  CAS  Google Scholar 

  41. Corish J, Morton-Blake DA, O’Donoghue F, Baudour JL, Bénière F, Toudic B (1995) J Mol Struct (Theochem) 358:29–38

    Article  CAS  Google Scholar 

  42. Wei-Guang Diau E (2004) J Phys Chem A 108:950–956

    Article  Google Scholar 

  43. Ishikawa T, Noro T, Shoda T (2001) J Chem Phys 115:7503–7512

    Article  CAS  Google Scholar 

  44. Cattaneo P, Persico M (1999) Phys Chem Chem Phys 1:4739–4744

    Article  CAS  Google Scholar 

  45. Fliegl H, Köhn A, Hättig C, Ahlrichs R (2003) J Am Chem Soc 125:9821–9827

    Article  CAS  Google Scholar 

  46. Mostad A, Romming C (1971) Acta Chem Scand 25:3561–3568

    Article  CAS  Google Scholar 

  47. http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

  48. Wilson EB (1934) Phys Rev 45:706–714

    Article  CAS  Google Scholar 

  49. Palafox MA (2000) Int J Quant Chem 77:661–684

    Article  CAS  Google Scholar 

  50. Schrerer JR, Overend J (1961) Spectrochim Acta 17:719–730

    Article  Google Scholar 

  51. Ilnytskyi JM, Neher D, Saphiannikova M (2011) J Chem Phys 135:044901–044913

    Article  Google Scholar 

  52. Duchstein P, Neiss C, Görling A, Zahn D (2012) J Mol Model 18:2479–2482

    Article  CAS  Google Scholar 

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Acknowledgments

We acknowledge computational time and support from CINECA under the ISCRA initiative. Funding from EU NanoSciE + project under the Transnational grant Maecenas is gratefully acknowledge. We thank M.A. Rampi, M. Persico, and G. Granucci for useful discussions.

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Correspondence to Stefano Corni.

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Online Resource 1

Complete set of FF parameters, extended tables for structural comparison with experiments, alternative sets of RESP charges, figures with MM and QM-PES comparison, experimental and QM vibrational spectra, mixed parameterization vibrational frequencies. (PDF 5656 kb)

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Pipolo, S., Benassi, E., Brancolini, G. et al. First-principle-based MD description of azobenzene molecular rods. Theor Chem Acc 131, 1274 (2012). https://doi.org/10.1007/s00214-012-1274-z

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  • DOI: https://doi.org/10.1007/s00214-012-1274-z

Keywords

  • Force field parameterization
  • DFT calculations
  • Azobenzenes
  • IR spectra