Interface Details




Query Molecule

The upper left contains a depiction of the current query molecule. A query molecule can be loaded by opening a file from the file combo box directly below the depiction, pasting from your favorite molecule editor, or by double clicking the depiction which launches the editor. The editor can accept both common molecule names and SMILES strings.



Once a molecule is loaded the application performs an “Analog Search.” The individual ionizable regions of the query molecule are highlighted. After the “Analog Search” is performed the ionizable regions become clickable, indicated by the highlighting color becoming more saturated when the mouse is hovered above. Clicking on a given ionizable region will limit the results to molecules that match that particular ionizable substructure. Clicking in the negative white space will return the full list of results.

The Query Molecule will persist between sessions.


Tautomer Selection

Tautomer Selection

If pKa-Prospector detects a more common tautomer for a given query molecule it will prompt the user to use the more common tautomer. Often search results will improve if the more common tautomer is used as the query molecule.

Property Filters

Property Filters

Property Filters

pKa and Temperature

The property filters below the query molecule depiction allow for filtering of the results that are displayed. Checking the “pKa Range” check box and setting the range sliders will limit the results displayed to only those measurements which fall within that range; likewise the “Temp Range” check box will also filter out measurements that do not fall between the provided ranges. The ranges can be set by either moving the range sliders or entering the desired numeric values in the spin boxes. The pKa filter range is limited between 0 and 14, the temperature filter range is limited from 0 and 50. Although there may be some data points that fall beyond these ranges these endpoints were chosen to allow for the maximum filter granularity of the vast majority of the data.

Ionization Types

By checking a subset of Acids, Bases, and Excited the results can be limited to showing measurements which have been assigned as falling into one of these categories.

Quality Minimum

Quality Quantities

Quality Quantities

The data has been annotated based upon the author’s assessment of quality, and the radio buttons allow for limiting the displayed results. There are a great deal more measurements on the lower end of the quality scale, so if ever it seems that the results list does not contain molecules that you believe should be there it helps to lower this threshold to hit upon a greater set of molecules.

Search Buttons

Show Additional Search Options

Show Additional Search Options

There are a total of five search options. By default only the “Analog Search” button is displayed. To get access to the full set, simply open the preferences dialog and then click “Show Additional Search Options” check box.

Search Buttons

Search Buttons

Results View

On the right hand side of the application is the results view.

Search Summary

The first row of the results view contains a depiction of the query molecule and a summary of the search, including any filters that were applied. If there is an exact match to the query molecule which passes the property filters this will always be in the second row.


The left hand column contains a depiction of the search results molecules. For an “Analog Search” the highlighting indicates the portion of the molecule which matches the ionizable region of the query molecule with the same color. For a “Substructure Search” the highlighting show the matching substructure. For a “Property Search” the highlighting corresponds to the resulting molecules individual ionizable regions, and is unrelated to any other molecules highlighting.

Double clicking the depiction will make the molecule the new query molecule.

Results Table

The right hand column contains a table enumerating all available measurements that pass the preference filter for the given molecule. Layout of the Results Table can be changed in the Preferences.

Double clicking the result table will open a detailed report of the selected molecule. More detail is given below.

The results view can be saved to PDF or CSV through the file menu.


Preference Dialog

Preference dialog

Results View Customization

The application’s preference dialog allows for the customization of the reported data columns. By checking items from the list titled “Results Table Headers” will affect how the results table is generated. The individual items can be reordered and that order will be respected within the results table.

Search Options

The “Show Additional Search Options” enables the “Substructure Search,” “Similarity Search,” “Exact Search,” and the “Property Search” options. The “Display Aqueous Determination Only” checkbox will cause the results to only ever display aqueous pKa values. The “Perform Search Automatically” checkbox will cause the application to perform the “Analog Search” automatically after any change to the query molecule.

Result Report

The Result Report is a detailed listing of all data which passes the property filter for a given result molecule. This window can remain open while performing other searches.

Result Report

Result Report


The molecular depiction has highlighting for the individual ionizable regions, independent of any other molecules and their highlighting.


The top right contains a short summary table with a few key fields, along with links to jump to the specific detailed report. The alternating background color of the summary table rows corresponds to the background color of the full data listing for that particular measurement.

Full Listing

The full listing contains all available data for that particular molecule. If data field is missing then that row will be omitted. The data fields are always in a fixed order.


The “Save to PDF” button will save the table to an easily printable PDF file including the depiction.

Appending Data

For institutions with their own pKa data, pKa-Prospector provides a means of folding that data into the user interface. It can live side by side with the IUPAC data.

Under the “File” menu there is an “Import Data...” dialog which will guide the user through the import process. The user has the option to name the imported database.

Data Loader

Data Loader

Data Formatting

In order for pKa-Prospector to properly import institutional data, the data must first be in an oeb or sdf file format with the desired measurement data set in SD data fields. The file is initially loaded through the dialogs “Open a file...” combo box. The application will then inspect the first 10 molecules to get a list SD data tags.

Data Mapping

The application requires that the various file SD data tags get associated to their corresponding properties. This is accomplished by using the pull down combo boxes. As any given data tag is assigned it will be removed from the lists under the other properties.

pKa Value: This is the only required data field; all others can have assumed default values. This field must be in a decimal format such that it can be converted using “float pka = atof(...);

Temp: Much like “pKa Value” this field must be easily converted to a float. The “Default Value” column is the value which will be assigned if there is no data tag assigned or if the assigned data tag is missing.

Ionization: This field must match the literal strings “Acid”, “Base”, “Excited” or “Unknown”. Much like temperature the default value can be set as well.

Assessment: This field must match the literal strings “reliable”, “uncertain”, or “approximate”. The default assignment can be set as well.

Aqueous: This fields indicates whether or not the pKa measurement was determined in aqueous solution. This field must be “0” or “1” for false or true satisfying “bool aqueous = (bool) atoi(...);

Extra Data

pKa-Prospector also allows for importing of extra data tags to be displayed along within results table. This may be useful in some cases, for example if a molecule or measurement is associated with a particular corporate id.

Selecting an Imported Database

Select Database

Select Database

Select Database

Once all the data fields are assigned and “OK” is clicked, pKa-Prospector will process the file and create an internal data file from where it can be loaded upon future sessions. After the conversion process is finished a dialog is displayed where various data bases can be selected. Currently the application allows for IUPAC and the user data or just the user data. If two imported databases have the same name the application will distinguish them by applying a time stamp. Also the user can delete an imported database by right clicking the database and selecting “Delete...” from context menu.

After the desired databases are selected the application will need to be restarted for the changes to take effect.



To cite pKa-Prospector please use the following:

pKa-Prospector OpenEye Scientific Software, Santa Fe, NM.