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European Pharmaceutical Journal

Acta Facultatis Pharmaceuticae Universitatis Comenianae (formerly)

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Comparison of different computational methods for water structure optimisation

R. Staník
  • Faculty of Pharmacy, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University, Bratislava
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/ P. Ballo
  • Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology
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  • De Gruyter OnlineGoogle Scholar
/ I. Benkovský
  • Faculty of Pharmacy, Department of Pharmaceutical Analysis and Nuclear Pharmacy, Comenius University, Bratislava
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  • De Gruyter OnlineGoogle Scholar
Published Online: 2012-08-13 | DOI: https://doi.org/10.2478/v10219-012-0019-3

Comparison of different computational methods for water structure optimisation

We have compared several computational techniques with the aim to compute the radial distribution function (RDF) as a good characterization of water structure. In particular, we have used molecular mechanic (AMBER99), semi-empirical (AM1, PM3, PM6) and ab initio (DFT) technique. It has been shown that molecular mechanic gives very poor results in the case of water RDF. Ab initio techniques which are in general accepted as very exact methods, in the case of water underestimate intermolecular interaction. Unexpectedly, the semi-empirical method with PM6 parameterisation gives the best results in comparison with RDF measured by X-ray scattering experiment.

Porovnanie Rôznych Výpočtových Metód Pre Optimalizáciu Štruktúry Vody

Porovnali sme niekoľko výpočtových techník s cieľom získať radiálnu distribučnú funkciu (RDF), ktorá je vhodná na charakteristiku štruktúry vody. Menovite sme použili molekulovú mechaniku (AMBER99), semi-empirické (AM1, PM3, PM6) a ab initio (DFT) techniky. Ukázalo sa, že molekulová mechanika poskytuje veľmi slabé výsledky vzhľadom na RDF vody. Ab initio techniky, ktoré sú všeobecne akceptované ako veľmi presné metódy, v prípade vody podceňujú medzimolekulové interakcie. Prekvapujíco, semi-empirickám metóda s PM6 parametrizáciou poskytuje najlepšie výsledky v porovnaní s meraním RDF pomocou X-ray rozptylu.

Keywords: water simulation; RDF; PM6; DFT

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About the article


Published Online: 2012-08-13

Published in Print: 2012-01-01


Citation Information: Acta Facultatis Pharmaceuticae Universitatis Comenianae, ISSN (Print) 0301-2298, DOI: https://doi.org/10.2478/v10219-012-0019-3.

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