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

TY - JOUR

T1 - Experimental equilibrium structures: Application of molecular dynamics simulations to vibrational corrections for gas electron diffraction

AU - Wann, D.A.

AU - Zakharov, A.V.

AU - Reilly, A.M.

AU - McCaffrey, P.D.

AU - Rankin, D.W.H.

N1 - Cited By (since 1996):11 Export Date: 1 October 2013 Source: Scopus CODEN: JPCAF 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: [email protected] References: Jensen, P., (1988) J. Mol Spectrosc, 128, p. 478; Jensen, P., (1988) J. Chem. Soc., Faraday Trans. 2, 84, p. 1315; Bastiansen, O., Traetteberg, (1960) M. Acta Crystallogr, 13, p. 1108; Breed, H., Bastiansen, O., Almenningen, A., (1960) Acta Crystallogr, 13, p. 1108; Morino, Y., (1960) Acta Crystallogr, 13, p. 1107; Hedberg, L., Mills, I.M., (1993) J. Mol Spectrosc, 160, p. 117; Hedberg, L., Mills, I.M., (2000) J. Mol Spectrosc, 203, p. 82; Sipachev, V.A., (1985) THEOCHEM, 22, p. 143; Sipachev, V.A., (1999) Advances in Molecular Structure Research, 5, pp. 323-371. , Hargittai, I. H. 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PY - 2009/8/27

Y1 - 2009/8/27

N2 - 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.

AB - 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.

KW - Anharmonic

KW - Anharmonic modes

KW - DFT method

KW - Empirical potentials

KW - Equilibrium geometries

KW - Equilibrium structures

KW - Field methods

KW - Gas electron diffraction

KW - General method

KW - Large deformations

KW - MD simulation

KW - Methyl group

KW - Molecular dynamics simulations

KW - Path integral method

KW - Path-integral

KW - Quantum effects

KW - Rigid molecules

KW - Starting values

KW - Test case

KW - Vibrational corrections

KW - Approximation theory

KW - Hydrocarbons

KW - Molecular dynamics

KW - Molecular vibrations

KW - Molecules

KW - Quantum electronics

KW - Electron diffraction

U2 - 10.1021/jp904185g

DO - 10.1021/jp904185g

M3 - Article

SN - 1089-5639

VL - 113

SP - 9511

EP - 9520

JO - Journal of Physical Chemistry A

JF - Journal of Physical Chemistry A

IS - 34

ER -