ACD/pKa Batch      Click image to magnify  Now Available for Linux

ACD/pKa Batch is a program that allows rapid and automatic calculation of acid-base ionization constants (pK_a values) for large sets of compounds at once. ACD/pK_a Batch has the same powerful and fast structure-fragment algorithm as ACD/pK_a DB, but it is stream-lined for large-scale users who require pK_a values for thousands of compounds at a time.

For each compound, ACD/pK_a Batch calculates the apparent pK_a values (those that are measured in aqueous solution at 25°C and at zero ionic strength) and/or single pK_a values (those that are measured for all possible dissociation centers when the rest of the molecule is considered neutral) at the specified pH range.
Note: the number of ionization centers in a molecule should not exceed 20.
Click here to find out about integration with Accelrys' Cerius² software.

With ACD/pK_a Batch you can:

• Calculate apparent or single pK_a values.
• Specify the pH range of interest.
• Calculate the most basic and most acidic pK_a values.
• Define amides or sulfonic/sulfuric groups as non-ionizable to speed up the calculation.
• Label the ionized groups and corresponding pK_a values (OH, NH group, etc.).
• Limit your calculation time per structure to ensure high throughput.

ACD/pK_a Batch has the same limitations as ACD/pK_a DB:

ACD/pK_a cannot calculate pK_a values for structures that:

• Contain more than 255 atoms (note that the program refuses to predict pK_a for some cyclic compounds having less than 255 atoms due to the fact that the program uses a cycle-breaking algorithm that increases the number of atoms).
• Contain more than 20 ionization centers.
• Contain no ionization centers.
• Contain atoms other than C, H, O, S, P, N, F, Cl, Br, I, Se, Si, Ge, Pb, Sn, As, and B.
• Contain atoms of non-typical valence.
• Contain two or more fragments.
• Contain d-block or f-block metal atoms.
• Contain textual abbreviations that cannot be transformed to structures fragments.

ACD/pK_a does not take into account the specific features of different stereomers (R-, S- isomerism), conformers, and isotopes.

This package is available for Microsoft Windows, SUN, and Linux platforms, and can be run from a Windows command line.

How ACD/pK_a Batch works:

I. Input file such as:

1. ACD/ChemFolder database (.CFD)
2. SMILES text file (.TXT)
3. MDL SDfile (.SDF)*
4. ISIS database (.DB)**

*Note: For more detail about this common text data exchange format, please refer to "MDL File Formats" at the MDL Inc. web site.
**Note: ISIS/Base 2.2 must be installed on the same PC. 

II. Set options:

1. Calculate apparent pK_a values.
2. Calculate single pK_a values.
3. Choose to calculate pK_a values at a specified pH range.
4. Calculate the most basic and most acidic pK_a values.
5. Treat certain groups as nonionazible.
6. Label pK_a values by functional groups.
7. Set a time limit for one structure calculation.

III. Choose to report results to .DB, .SDF, .RDF, .CFD, or .TXT files.