User guide

pKa, CLogP, and CMR
Specific algorithms for calculating LogP and molar refractivity from fragment-based methods developed by the Medic-
inal Chemistry Project and BioByte. For more information, see http://www.biobyte.com/blqsar/index.html.
LogP and CLogP estimate the Octanol/Water Partition Coefficient, but use different methods.
CLogP and CMR are calculated as part of the Chemical Properties window. Several other sources exist for LogP
data, however:
The ChemBioDraw report window for LogP prediction
The Chemical Properties window shows averaged LogP and MR values. Via the "Report" button, you can see the orig-
inal values from each applicable estimation method. The estimation methods are Crippen's fragmentation, Vis-
wanadhan's fragmentation, and Broto's method.
The ChemBioDraw report window for LogP empirical data
For selected substances, the Chemical Properties window's "Report" button includes a section "Data from data-
base," which includes measured values of the partition coefficient and pKa values, at specified pH levels, with source
citations.
The ChemBioDraw ChemBioFinder hotlink window
Several available databases include LogP and pKa information, including:
The Merck Index includes empirical pK data for selected compounds.
ChemSpider (from InChI link) predicts several variations of LogP and LogD.
ChemINDEX (Physical Properties section, Environment Science Center database) includes empirical pKa and
LogP data
ChemDraw/Excel
The ChemDraw add-in module in Excel predicts:
LogP (function CHEMPROPPRO_LOGP)
CLogP (function CLOGP_DRIVER_PARTITION_COEFFICIENT).
MR (function CHEMPROPPRO_ MOL_REFRACTIVITY)
CMR (function CLOGP_DRIVER_MOL_REFRACTIVITY).
ChemBioFinder/ChemBioViz
The Property Populator predicts:
LogP (server ChemPropPro, property LogP)
CLogP (server CLogP driver, property Partition_Coefficient)
MR (server ChemPropPro, property Mol Refractivity)
CMR (server CLogP driver, property Mol Refractivity).
ChemBio3D
The Property Picker predicts:
LogP (ChemPropPro LogP)
ChemBioDraw 13.0
Chapter 16: Property calculations 302 of 401