First-principle-based MD description of azobenzene molecular rods

Silvio Pipolo, Enrico Benassi, Giorgia Brancolini, Michal Valášek, Marcel Mayor, Stefano Corni

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)


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 selfassembled monolayers (SAMs) of azobenzene's molecular rods, as well as to the quantum mechanics/molecular mechanics study of photoisomerization in SAMs.

Original languageEnglish
Pages (from-to)1-14
Number of pages14
JournalTheoretical Chemistry Accounts
Issue number10
Publication statusPublished - 4 Oct 2012
Externally publishedYes


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

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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