Revision as of 03:10, 25 December 2014

Atomic charges are non-integer numbers quantifying the balance of positive (nuclear) charge and negative (electronic) charge associated with each atom. In the 3D space, atomic charges represent points placed at the position of the atomic nuclei, and may be termed atomic point charges. The molecular representation based on atomic point charges is thus a very basic abstraction of the molecular electron density. Moreover, having only a conceptual character, there is no unique definition of atomic charges. Rather, a score of such definitions have been published and are in use.

ACC is able to calculate atomic charges on molecules of any nature and size based on empirical models. What one can do with the resulting atomic charges strongly depends on the principles behind the definition of the atomic charge concept used in the development of the empirical model. Be sure to also check out the Frequently Asked Questions section for additional information.

While atomic charges are merely concepts and not physical observables, they have been used heavily in theoretical and applied chemistry due to their highly intuitive character and correlation with measurable quantities such as the electrostatic potential, polarity, reactivity, etc. Nowadays, atomic charges are still integral parts of many modeling applications, and are still used in reasoning basic chemical processes. Below you can find a few tips regarding the main applications of atomic charges in understanding and modeling the chemical behavior of molecules. This is by no means an exhaustive list. It is useful to keep an open mind with respect to potential applications, while being aware of the limitations inherent to the atomic point charge model.

Understand chemical reactivity

Many reaction mechanisms rely on a surplus of positive or negative charge at a certain site in the molecule. For instance, a nucleophylic attack happens at a positively charged site. In simple molecules like tert-butyl bromide, such sites are easy to identify by electron induction effects. However, as molecules become more complex, it is difficult to distinguish potential reaction sites based solely on concepts like induction and conjugation, because they are not quantitative. A simple atomic charge calculation can easily identify potential reaction sites.

Such a concept can be extended to biochemically interesting sites. Due to charge transfer and polarizability, total residue charges will deviate from the expected formal values (-1,0,1). Specific residues which are significantly more positive or negative than their surroundings are more likely to be the site of post translational modifications. Some salt bridges are stronger than others, and it is possible to predict which salt bridges can be more easily disrupted.

Analyze charge transfer pathways

While the absolute values of atomic charges cannot be validated experimentally, and even when they themselves do not correlate with any phenomenon observable for a certain molecular system under given conditions available to the user (or in literature), it is possible that the relative differces in charges hold further information about chemical reactivity and biological significance. Given two states of the same system, calculate the charges, look for patterns - atoms, residues or other types of molecular fragments (e.g., multiple water molecules in the binding site) for which the charge varies significantly between the two states.

Quantitative Structure-Property Relationships modelling

QSPR for various properties - pharmacokinetics... pKa example? Atomic charges can be used as descriptors, generally in combination with various other descriptors (based on the molecular topology, 3D structure, electronic structure, etc.)

Generating molecular conformations

Docking

Molecular Mechanics simulations

explain FF compatibility Currently, ACC does not provide input files specific to each simulation package, mainly because there are too many of them, each different and continuously evolving. However, ACC provides molecular structure files containing charges (mol2, pqr), as well as files containing only charges (.mchrg) which can be easily incorporated in other file formats.

Start by having a look at the main terms used by ACC, or return to the Table of contents.

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 Many reaction mechanisms rely on a surplus of positive or negative charge at a certain site in the molecule. For instance, a nucleophylic attack happens at a positively charged site. In simple molecules like tert-butyl bromide, such sites are easy to identify by electron induction effects. However, as molecules become more complex, it is difficult to distinguish potential reaction sites based solely on concepts like induction and conjugation, because they are not quantitative. A simple atomic charge calculation can easily identify potential reaction sites.
-Such a concept can be extended to biochemically interesting sites. Due to charge transfer and polarizability, total residue charges will deviate from the expected formal values (-1,0,1). Some salt bridges are stronger than others, since the interaction is stronger if the residues involved have higher charge. Therefore, one can predict which salt bridges can be more easily disrupted.
+Such a concept can be extended to biochemically interesting sites. Due to charge transfer and polarizability, total residue charges will deviate from the expected formal values (-1,0,1). Specific residues which are significantly more positive or negative than their surroundings are more likely to be the site of post translational modifications. Some salt bridges are stronger than others, and it is possible to predict which salt bridges can be more easily disrupted.
 =Analyze charge transfer pathways=