Editing ChargeCalculator:FAQ (section)

=How do I read the XML file with EEM parameters?=

EEM, the empirical method used by '''ACC''' to calculate atomic charges, relies on empirical parameters. Many EEM parameter sets have been published in literature, and are available in '''ACC''' as ''built-in sets''. EEM parameter sets are stored in XML format, where the information is organized using tags. Each type of useful information is marked by a start and an end tag, may have attributes and may contain sub-elements or text.

Each EEM parameter set is marked by the ''ParameterSet'' tag and the attribute ''Name'', which encodes a unique identifier. Further, each EEM parameter set is described by properties marked by the ''Properties'' tag, which provide the literature reference and basic information about the development of the EEM parameters. Please read the section on [[ChargeCalculator:FAQ#How_do_I_choose_a_suitable_EEM_parameter_set.3F | how to choose a suitable EEM parameter set]] in order to better understand the importance of the information given by ''Properties''.

Next, the EEM parameters are given under the tag ''Parameters'', which has three attributes. ''Target'' and ''Priority'' are important for [[ChargeCalculator:FAQ#How_do_I_choose_a_suitable_EEM_parameter_set.3F | choosing a suitable EEM parameter set]]. The attribute ''Kappa'' is actually a [[ChargeCalculator:Theoretical_background#EEM | special EEM parameter]] which, conceptually, modulates the electrostatic interaction of each atom with the surrounding charges. 

<ParameterSet Name="Bult2002_npa">
  <Properties>
    <Property Name="Author">Bultinck, P., Langenaeker, W., Lahorte, P., De Proft, F., Geerlings, P., Waroquier, M., Tollenaere, J. P.</Property>
    <Property Name="Publication">The Electronegativity Equalization Method II: Applicability of Different Atomic Charge schemes</Property>
    <Property Name="Journal">J. Phys. Chem. A, 106, 7895-7901</Property>
    <Property Name="Year">2002</Property>
    <Property Name="Target">Organic molecules</Property>
    <Property Name="QM Method">B3LYP</Property>
    <Property Name="Basis Set">6-31G*</Property>
    <Property Name="Population Analysis">NPA</Property>
    <Property Name="Training Set Size">138</Property>
    <Property Name="Data Source">Not Specified</Property>
    <Property Name="Priority">4</Property>
  </Properties>
  <UnitConversion KappaFactor="0.529177249000" ABFactor="0.036749309000" />
  <Parameters Target="Atoms" Priority="0" Kappa="1.000000000000">
    <Element Name="C">
      <Bond Type="1" A="8.490000000000" B="18.300000000000" />
      <Bond Type="2" A="8.490000000000" B="18.300000000000" />
      <Bond Type="3" A="8.490000000000" B="18.300000000000" />
    </Element>
    <Element Name="F">
      <Bond Type="1" A="39.180000000000" B="88.200000000000" />
    </Element>
    ...
  </Parameters>
 </ParameterSet>

The rest of the EEM parameters operate with atom types based on chemical elements, and are marked by the ''Element'' tags. However, some EEM parameter sets available in literature employ atom types which depend not only on chemical element, but also on the maximum ''bond multiplicity''. In such EEM parameter sets there are, for example, different EEM parameters for carbon atoms with sp&sup3; hybridization, than for carbon atoms with sp&sup2; hybridization. In order to keep a consistent scheme of storing and assigning parameters, '''ACC''' implements by default an EEM parameter scheme which supports bond information via the ''Bond'' tag. Thus, for each chemical element there will be one ''Element'' tag, and at least one ''Bond'' tag. EEM parameter sets which are based solely on chemical elements and no bond information contain multiple ''Bond'' tags as well, but the parameters associated with different bond multiplicities (the attribute ''Type'') are actually merely copies, as seen in the example above.

The attribute ''Type'' encodes the maximum bond multiplicity. In general, sp&sup3; hybridization is encoded as ''Type=1'', sp&sup2; hybridization as ''Type=2'', and sp hybridization as ''Type=3''. These values might seem unintuitive, but they are based on connectivity information from the input file, or computed based on interatomic distances. ''Type=0'' encodes a coordinated metal ion.

The actual [[ChargeCalculator:Theoretical_background#EEM | EEM parameters]] are encoded in the attributes ''A'' and ''B'', conceptually related to electronegativity and hardness, respectively.

Note also the ''Unit conversion'' tag used to unify the values of the parameters from different sources in literature. The attribute ''KappaFactor'' is the correction applied to the ''Kappa'' parameter, while the attribute ''ABFactor'' is the correction applied to the values of parameters ''A'' and ''B''. In the example above, the electronegativity and hardness and parameters (''A'' and ''B'', respectively) were originally given in eV, while the atomic distances were given in atomic units. '''ACC''' uses parameters ''A'' and ''B'' in relative units (Hartrees), and atomic distances in Angstroms. The conversion factors are:
<pre>
1 Hartree = 27.2114 eV
1 atomic unit = 0.529177249 Angstroms
</pre>
Therefore, the following corrections will be applied to the EEM parameters. The ''Kappa'' parameter will be corrected by a ''KappaFactor'' of 0.529177249. The ''A'' and ''B'' parameters will be corrected by an ''ABFactor'' of 0.036749309 (1/27.2114).