Experimental equilibrium structures: Application of molecular dynamics simulations to vibrational corrections for gas electron diffraction

D.A. Wann, A.V. Zakharov, A.M. Reilly, P.D. McCaffrey, D.W.H. Rankin

Research output: Contribution to journalArticlepeer-review


A general method is described that allows experimental equilibrium structures to be determined from gas electron diffraction (GED) data. Distance corrections, starting values for amplitudes of vibration and anharmonic "Morse" constants (all required for a GED refinement) have been extracted from molecular dynamics (MD) simulations. For this purpose MD methods have significant advantages over traditional force-field methods, as they can more easily be performed for large molecules, and, as they do not rely on extrapolation from equilibrium geometries, they are highly suitable for molecules with large-amplitude and anharmonic modes of vibration. For the test case Si 8O 12Me 8, where the methyl groups rotate and large deformations of the Sig 8O 12 cage are observed, the MD simulations produced results markedly superior to those obtained using forcefield methods. The experimental equilibrium structure of Si 8O 12H 8 has also been determined, demonstrating the use of empirical potentials rather than DFT methods when such potentials exist. We highlight the one major deficiency associated with classical MD-the absence of quantum effects-which causes some lightatom bonded-pair amplitudes of vibration to be significantly underestimated. However, using C 3N 3Cl 3 and C 3N 3H 3 as examples, we show that path-integral MD simulations can overcome these problems. The distance corrections and amplitudes of vibration obtained for C 3N 3Cl 3 are almost identical to those obtained from force-field methods, as we would expect for such a rigid molecule. In the case of C 3N 3H 3, for which an accurate experimental structure exists, the use of path-integral methods more than doubles the C-H amplitude of vibration. © 2009 American Chemical Society.
Original languageUndefined/Unknown
Pages (from-to)9511-9520
Number of pages10
JournalJournal of Physical Chemistry A
Issue number34
Publication statusPublished - 27 Aug 2009

Bibliographical note

Cited By (since 1996):11

Export Date: 1 October 2013

Source: Scopus


doi: 10.1021/jp904185g

Language of Original Document: English

Correspondence Address: Rankin, D. W. H.; School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom; email: d.w.h.rankin@ed.ac.uk

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  • Anharmonic
  • Anharmonic modes
  • DFT method
  • Empirical potentials
  • Equilibrium geometries
  • Equilibrium structures
  • Field methods
  • Gas electron diffraction
  • General method
  • Large deformations
  • MD simulation
  • Methyl group
  • Molecular dynamics simulations
  • Path integral method
  • Path-integral
  • Quantum effects
  • Rigid molecules
  • Starting values
  • Test case
  • Vibrational corrections
  • Approximation theory
  • Hydrocarbons
  • Molecular dynamics
  • Molecular vibrations
  • Molecules
  • Quantum electronics
  • Electron diffraction

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