This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.

Force Field for the Cofactors of Bacterial Photosynthesis / MATTEO CECCARELLI; P. PROCACCI; MASSIMO MARCHI. - In: JOURNAL OF COMPUTATIONAL CHEMISTRY. - ISSN 0192-8651. - STAMPA. - 24:(2003), pp. 129-142.

Force Field for the Cofactors of Bacterial Photosynthesis

PROCACCI, PIERO;
2003

Abstract

This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.
2003
24
129
142
MATTEO CECCARELLI; P. PROCACCI; MASSIMO MARCHI
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Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/219749
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