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First-principle-based MD description of azobenzene molecular rods

Theoretical Chemistry Accounts volume 131, Article number: 1274 (2012) Cite this article

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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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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Authors and Affiliations

  1. Centro S3, CNR Istituto di Nanoscienze, via G. Campi 213/a, 41125, Modena, Italy

    Silvio Pipolo, Enrico Benassi, Giorgia Brancolini & Stefano Corni

  2. Dipartimento di Fisica, Università di Modena e Reggio Emilia, via G. Campi 213/a, 41125, Modena, Italy

    Silvio Pipolo

  3. Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany

    Michal Valášek & Marcel Mayor

  4. Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland

    Marcel Mayor

Authors
  1. Silvio Pipolo
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  2. Enrico Benassi
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  3. Giorgia Brancolini
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  4. Michal Valášek
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  5. Marcel Mayor
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  6. Stefano Corni
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Corresponding author

Correspondence to Stefano Corni.

Electronic supplementary material

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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