The ability of caffeic acid to act as antioxidant against hyperoxo-radicals as well as its recently found therapeutic properties in the treatment of hepatocarcinoma, still make this compound, more than 20 years later the refinement of its crystal structure, object of study. It belongs to the vast family of humic substances, which play a key role in the biodegradation processes and easily form complexes with ions widely diffused in the environment. This class of compounds is therefore interesting for potential environmental chemistry applications concerning the possible complexation of heavy metals. Our study focused on the characterization of caffeic acid as a starting necessary step, which will be followed in the future by the application of our findings on the study of the properties of caffeate anion interaction with heavy metal ions. To reach this goal, we applied a low cost approach - in terms of computational time and resources aimed at the achievement of a high resolution, robust and trustable structure using the X-ray single crystal data, recollected with a higher resolution, as touchstone for a detailed check. A comparison between the calculations carried out with density functional theory (DFT), Hartree-Fock (HF) method and post SCF second order Moller-Plesset perturbation method (MP2), at the 6-31G** level of the theory, molecular mechanics (MM) and molecular dynamics (MD) was performed. As a consequence we explained on one hand the possible reasons for the pitfalls of the DFT approach and on the other the benefits of using a good and robust force field developed for condensed phases, as AMBER, with MM and MD. The reliability of the latter, highlighted by the overall agreement extended up to the anisotropic displacement parameters calculated by means of MD and the ones gathered by X-ray measurements, makes it very promising for the above-mentioned goals. (C) 2011 Elsevier B.V. All rights reserved.

From the X-rays to a reliable “Low cost” computational structure of caffeic acid: DFT, MP2, HF and integrated molecular dynamics X-ray diffraction approach to condensed phases / Giuseppe M., Lombardo; Portalone, Gustavo; Colapietro, Marcello; Antonio, Rescifina; Francesco, Punzo. - In: JOURNAL OF MOLECULAR STRUCTURE. - ISSN 0022-2860. - STAMPA. - 994:1-3(2011), pp. 87-96. [10.1016/j.molstruc.2011.03.001]

From the X-rays to a reliable “Low cost” computational structure of caffeic acid: DFT, MP2, HF and integrated molecular dynamics X-ray diffraction approach to condensed phases

PORTALONE, Gustavo;COLAPIETRO, Marcello;
2011

Abstract

The ability of caffeic acid to act as antioxidant against hyperoxo-radicals as well as its recently found therapeutic properties in the treatment of hepatocarcinoma, still make this compound, more than 20 years later the refinement of its crystal structure, object of study. It belongs to the vast family of humic substances, which play a key role in the biodegradation processes and easily form complexes with ions widely diffused in the environment. This class of compounds is therefore interesting for potential environmental chemistry applications concerning the possible complexation of heavy metals. Our study focused on the characterization of caffeic acid as a starting necessary step, which will be followed in the future by the application of our findings on the study of the properties of caffeate anion interaction with heavy metal ions. To reach this goal, we applied a low cost approach - in terms of computational time and resources aimed at the achievement of a high resolution, robust and trustable structure using the X-ray single crystal data, recollected with a higher resolution, as touchstone for a detailed check. A comparison between the calculations carried out with density functional theory (DFT), Hartree-Fock (HF) method and post SCF second order Moller-Plesset perturbation method (MP2), at the 6-31G** level of the theory, molecular mechanics (MM) and molecular dynamics (MD) was performed. As a consequence we explained on one hand the possible reasons for the pitfalls of the DFT approach and on the other the benefits of using a good and robust force field developed for condensed phases, as AMBER, with MM and MD. The reliability of the latter, highlighted by the overall agreement extended up to the anisotropic displacement parameters calculated by means of MD and the ones gathered by X-ray measurements, makes it very promising for the above-mentioned goals. (C) 2011 Elsevier B.V. All rights reserved.
caffeic acid; molecular dynamics and x-ray diffraction data comparison; symmetry and anisotropic displacement parameters prediction; computational methods efficiency
01 Pubblicazione su rivista::01a Articolo in rivista
From the X-rays to a reliable “Low cost” computational structure of caffeic acid: DFT, MP2, HF and integrated molecular dynamics X-ray diffraction approach to condensed phases / Giuseppe M., Lombardo; Portalone, Gustavo; Colapietro, Marcello; Antonio, Rescifina; Francesco, Punzo. - In: JOURNAL OF MOLECULAR STRUCTURE. - ISSN 0022-2860. - STAMPA. - 994:1-3(2011), pp. 87-96. [10.1016/j.molstruc.2011.03.001]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/90108
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