Charge, atomic Gasteiger-Marsili

The first term in Eqs. [28]-[31] is related to hydrophobicity, whereas hydrophilicity is encoded by the others terms. The third term in Eqs. [30] and [31] is introduced to incorporate effects of molecular polarizability. Calculations of partition coefficients for 90 model compounds indicate that Eq. [30] is the best one and that a fast and cheap method to calculate atomic charges (e.g., the Gasteiger-Marsili approach>26) is perfectly adequate. The accuracy obtained with Eq. [30] is comparable to that reported by Bodor et al. 29,i3o addition, this method yields distinct values for geometric isomers or different conformers of flexible compounds, indicating that it is able to determine the influence of 3D arrangements of atoms on the overall lipophilic character of a structure. 

When using a force field evaluation function, partial atomic charges are required. For the DOCK suite of programs, for example, Gasteiger-Marsili partial charges using the program Sybyl (Tripos Associates, St. Louis, MO) are used. 

Here, and Lj are local indices having the form shown in Eq. (5), where lo is a constant characterizing the ith atom (in some cases the atom valence can be used to this end), Nh is the number of attached hydrogen atoms and is the charge density calculated by some fast method such as the Marsili-Gasteiger charge calculation method [7]. 

Gasteiger J and M Marsili 1980. Iterative Partial Equalization of Orbital Electronegativity - Rapid Access to Atomic Charges. Tetrahedron 36 3219-3288. 

Gasteiger, J., Marsili, M. Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 1980, 36, 3219-3228. 

Gasteiger J, Marsili M. A new model for calculating atomic charges in molecules. Tetrahedron Lett, 1978 3181-3184. 

Some methods calculate atomic charges solely from information about the atoms present in the molecule and the way in which the atoms are connected. The great advantage of such methods is that they are very fast and can be used to calculate the charge distributions for large numbers of molecules (e.g. in a database). We will consider the Gasteiger and MarsiU method [Gasteiger and Marsili 1980] as an example. 

Bijcxpi-Cijnj). The atomic charges are considered according to the methods of Smith or Gasteiger and Marsili. ROTEN is a modified version from ROTENER (1996) with ATOMCHAR (1995). ... 

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