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Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models

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Abstract

In this paper, a computational strategy, based on DFT calculations at the M06-2X level, combined with the polarizable continuum model, the Hessian matrix reconstruction method and the Partial hessian vibrational approach is applied to evaluate inter- and intra-layer vibrational couplings between hydrogen bonded and stacked DNA base pairs. The present work demonstrates that this computational scheme can effectively predict and interpret the vibrational couplings of nucleic acids in solution. The effect of the environment described in a cluster or in a continuum manner is necessary in order to improve the agreement with the experimental values.

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Authors and Affiliations

  1. Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento, 35, 56126, Pisa, Italy

    Alessandro Biancardi, Chiara Cappelli, Benedetta Mennucci & Jacopo Tomasi

  2. Dipartimento di Chimica GIAF, Università di Parma, viale delle Scienze, 43100, Parma, Italy

    Roberto Cammi

Authors
  1. Alessandro Biancardi
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  2. Roberto Cammi
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  3. Chiara Cappelli
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  4. Benedetta Mennucci
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  5. Jacopo Tomasi
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Corresponding author

Correspondence to Jacopo Tomasi.

Additional information

Dedicated to Professor Vincenzo Barone and published as part of the special collection of articles celebrating his 60th birthday.

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Biancardi, A., Cammi, R., Cappelli, C. et al. Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models. Theor Chem Acc 131, 1157 (2012). https://doi.org/10.1007/s00214-012-1157-3

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  • DOI: https://doi.org/10.1007/s00214-012-1157-3

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