ACD/LogP DB

Technical Information

Algorithm

All ACD/LogP programs—ACD/LogP DB, ACD/PhysChem Batch (LogP module), and ACD/LogD Suite (LogP module)—have the unique additive-constitutive ACD/LogP algorithm in common.

The ACD/LogP algorithm is based on well-characterized logP contributions of separate atoms, structural fragments, and intramolecular interactions between different fragments. These contributions have been derived from >25,000 compounds for which one or more experimental logP values were available to us. A subset of this database of experimental values collected from the public domain—the logP reference database—can be directly searched and viewed.

The most reliable logP increments are stored in the internal training dataset of logP contributions:

• The database of fragmental contributions contains well-characterized increments for >1200 different functional groups. These differ from each other by their chemical structure (e.g., amide, carboxy, ester, etc.), attachment to the hydrocarbon skeleton (aliphatic, vinylic, or aromatic), cyclization (cyclic or non-cyclic), and aromaticity (non-aromatic, aromatic, or fused aromatic).
• The database of carbon atom contributions contains well-characterized increments for different types of carbon atoms that are not involved in any functional group. They differ from each other by their state of hybridization (sp, sp², or sp³), number of attached hydrogens or branching (primary, secondary, tertiary, or quaternary), cyclization (cyclic or non-cyclic), and aromaticity (non-aromatic, aromatic, or fused aromatic).
• The database of the intramolecular interaction contributions contains well-characterized increments for >2400 different types of pair-wise group interactions. They differ from each other by the type of the interacting terminal groups (see the differences among functional groups above), and the length and type of the fragmental system in-between the interacting groups (aliphatic, aromatic, and vinylic).

If, during logP calculation, some of the fragmental or intramolecular interaction contributions are not found in the internal databases, they are calculated by "secondary" algorithms. In such cases the calculated logP values are provided with larger uncertainty limits. A warning appears in the Results Window, along with 'approximated value' indicators for relevant increments.

When you create a User Database with your own structures, the program automatically "splits" them into a set of unique fragments. As you assign new logP/logD values to structures, the program treats this data as an update to its internal database.

Limitations of the ACD/LogP Algorithm

• Charged structures containing IV-valent Nitrogen (+), except for the non-ionic derivatives of IV-valent Nitrogen (+) bonded to Oxygen (-) or bonded to Nitrogen (-) with a double bond (note that such compounds can be calculated, if their logP values are included in the user database that is used for system training).
• Structures containing atoms other than C, H, O, S, N, and F in reasonable chemical surroundings or structures containing atoms P, Cl, Br, I, Se, Si, Ge, Pb, Sn, As, or B that are not within the chemical surroundings shown below (note that A denotes any atom out of C, O, S, N, F, or any group listed below):

• Structures that contain elements in their non-typical valence.
• Structures with coordinating bonds.
• Structures containing more than 255 atoms excluding hydrogen.

Notes:

• The groups from the table cannot be a part of a cycle unless otherwise is stated.
• The group marked with an asterisk can be part of an aromatic cycle.

The program does not take into account the specific features of different geometric isomers, stereoisomers, conformers, isotopes, and structures with non-covalent bonds.

Since R&D usually involves novel chemical space, it is possible that specific structural features, such as far-range non-covalent bonding, intra-molecular shielding, or inter-molecular association, are not covered by the existing algorithm. For such cases, use of system training or ACD/PhysChem Accuracy Extender (logP module) is highly recommended.