User guide

Property calculations
You can calculate predicted values of selected physical and thermodynamic properties for structures of up to 200
heavy atoms. This section describes how the values are determined.
LogP
Three fragmentation methods are used to predict the logP values.
Method one is based on 94 atomic contributions evaluated from 830 molecules by least squares analysis. This
method works with a standard deviation of 0.47 logP units and can handle molecules containing hydrogen, oxygen,
nitrogen, sulfur and halogens.
Method two is an extension of method one but is based on 120 atomic contributions evaluated from 893 molecules
by least squares analysis. In addition to the atoms introduced for method one, it can handle molecules that contain
phosphorus and selenium atoms. This method works with a standard deviation of 0.50 logP units.
Method three is based on 222 atomic contributions calculated from 1868 molecules by least squares analysis. This
method allows a calculation of logP with a standard deviation of 0.43 logP units and can handle molecules con-
taining hydrogen, oxygen, nitrogen, sulfur, halogens and phosphorus atoms. If this method is applied to molecules
with internal hydrogen bonds, the standard deviation is 0.83 LogP units.
Henry’s law
Two methods are used to predict Henry’s Law constant.
The first is an approach based on the bond contribution method. This method uses 59 bond contribution values and
15 correction factors. The contributions were calculated by least squares analysis using a data set of 345 chem-
icals. This method estimates with a mean error of 0.30 units and a standard deviation of 0.45 units and can handle
molecules containing carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus and halogens.
In the second method, Henry’s Law constant is estimated from an equation found using linear regression. Mul-
tifunctional compounds were omitted from this study. This method should not be used for compounds where distant
polar interaction is present.
Molar refractivity
Two fragmentation methods are used to estimate the molar refractivity value.
Method one includes 93 atomic contributions evaluated from 504 molecules by using a constrained least squares
technique. This method works with a standard deviation 1.27 cm
3
/mol and can handle molecules containing
hydrogen, oxygen, nitrogen, sulfur and halogens.
The second method is an extension of method one that includes 120 atomic contributions evaluated from 538 mole-
cules by using a constrained least squares analysis technique. In addition to the atoms introduced for method one,
this method can handle molecules with phosphorus and selenium atoms. This method works with a standard devi-
ation of 0.77 cm
3
/mol.
ChemBioDraw 13.0
Chapter 16: Property calculations 301 of 401