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Issue 29, 2009
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A modified electronegativity equalization method for fast and accurate calculation of atomic charges in large biological molecules

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Abstract

To further extend the EEM approach to improve its accuracy, a new approach, in which the different connectivities and hybridized states are introduced to represent the different chemical environments, has been developed. The C, O and N atoms are distinguished between different hybridized states. Different states of hydrogen atoms are defined according to their different connectivities. Furthermore, the sp2 carbons in the aromatic rings are also separated from the other sp2 carbons. Geometries and NPA charges are calculated at the B3LYP/6-31G* level, and the effective electronegativity and hardness values could be calibrated with the help of a training set of 141 organic molecules using the Differential Evolution (DE) algorithm. The quality of the modified EEM charges is evaluated by comparison with the B3LYP/6-31G* charges calculated for a series of polypeptides, not contained in the training set. For further comparison, the atomic parameters of the original EEM without including chemical environments are recalibrated under the same conditions. It is found that the accuracy of the modified EEM method improves significantly as compared to that of the original EEM method.

Graphical abstract: A modified electronegativity equalization method for fast and accurate calculation of atomic charges in large biological molecules

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Publication details

The article was received on 03 Dec 2008, accepted on 07 May 2009 and first published on 26 May 2009


Article type: Paper
DOI: 10.1039/B821696G
Citation: Phys. Chem. Chem. Phys., 2009,11, 6082-6089
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    A modified electronegativity equalization method for fast and accurate calculation of atomic charges in large biological molecules

    Y. Ouyang, F. Ye and Y. Liang, Phys. Chem. Chem. Phys., 2009, 11, 6082
    DOI: 10.1039/B821696G

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